diff --git a/.travis.yml b/.travis.yml
index def8304a282f6c866baeae964c2d67e7d1ef1fba..97a59ca39e9c6815a110cc3c0a62d90e0011f2ab 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -79,7 +79,7 @@ matrix:
- $HOME/.macports-ci-ccache
# osx serial macports debug variant
- os: osx
- osx_image: xcode8.2
+ osx_image: xcode8.3
env: PLUMED_MACPORTS="plumed +allmodules +python27"
cache:
directories:
@@ -141,7 +141,7 @@ install:
# then replace doxygen with the desided version
# I use 1.8.10 instead of 1.8.11 since it looks like 1.8.11 have troubles with
# non case sensitive files (it writes capitalized filenames)
- - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_13 ; fi
+ - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_14 ; fi
- if test "$VALGRIND" == yes ; then sudo apt-get install -y valgrind ; fi
- if test "$LAPACK" == yes ; then sudo apt-get -y install libatlas-base-dev ; fi
# moreover, we hardcode path to dynamic library, required for xdrfile to link properly
@@ -183,7 +183,8 @@ script:
# build using macports
- if test -n "$PLUMED_MACPORTS" ; then
- sudo port -N install $PLUMED_MACPORTS ;
+ sudo port -N -k install $PLUMED_MACPORTS ;
+ plumed config show
./macports-ci ccache --save ;
fi
@@ -193,7 +194,7 @@ script:
# TEST:
- if test "$VALGRIND" == yes ; then OPT=valgrind ; else OPT="" ; fi
# --no-print-directory make it more silent
- - if test "$PLUMED_CXX" || test -n "$PLUMED_MACPORTS" ; then make --no-print-directory -C regtest $OPT ; fi
+ - if test "$PLUMED_CXX" ; then make --no-print-directory -C regtest $OPT ; fi
# test with gcc6
- if test "$PLUMED_DOCKER" = yes ; then docker run -v "$PWD/regtest":/home/plumed/regtest -it plumed /bin/bash -c "make -C regtest" ; fi
@@ -202,7 +203,8 @@ script:
- if test "$MAKEDOC" == yes ; then make -C regtest copytodoc ; fi
- if test "$MAKEDOC" == yes ; then make -C developer-doc coverage ; fi
- if test "$MAKEDOC" == yes ; then make doc >/dev/null ; fi
- - if test "$PLUMED_CXX" || test -n "$PLUMED_MACPORTS" ; then make -C regtest checkfail ; fi
+ - if test "$PLUMED_CXX" ; then make -C regtest checkfail ; fi
+ - if test -n "$PLUMED_MACPORTS" ; then sudo port -N -d test $PLUMED_MACPORTS ; fi
# CPPCHECK:
# this is required so as to have all the include files inplace:
diff --git a/.travis/install.cppcheck b/.travis/install.cppcheck
index 2880723e24c126dc626472abed9acdaefb06284a..767c23608e0f9cb1ae22482163b880293fb329d5 100755
--- a/.travis/install.cppcheck
+++ b/.travis/install.cppcheck
@@ -3,7 +3,7 @@
set -e
set -x
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
git clone https://github.com/danmar/cppcheck.git
cd cppcheck
diff --git a/.travis/install.doxygen b/.travis/install.doxygen
index 1f020a22e0a5d7e0aa9b17b68fac69811c4642e1..f62bda74d2d24ca4df78e124f68ebfe6add9ef92 100755
--- a/.travis/install.doxygen
+++ b/.travis/install.doxygen
@@ -3,7 +3,7 @@
set -e
set -x
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
git clone https://github.com/doxygen/doxygen.git
diff --git a/.travis/install.gawk b/.travis/install.gawk
index d7fdf6edf2ff42d8ce8ab37c6564d9a8e0064d45..d2eb4386684073ec3ced26d1640f1da84d119edd 100755
--- a/.travis/install.gawk
+++ b/.travis/install.gawk
@@ -3,7 +3,7 @@
set -e
set -x
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
version=4.1.4
diff --git a/.travis/install.lcov b/.travis/install.lcov
index dc38f3a2583867a1a2cb8655100d82f4a9d90906..4df4f61b815e11116952e834ab94dcf8497f8270 100755
--- a/.travis/install.lcov
+++ b/.travis/install.lcov
@@ -3,7 +3,7 @@
set -e
set -x
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
git clone https://github.com/linux-test-project/lcov.git
diff --git a/.travis/install.xdrfile b/.travis/install.xdrfile
index 296a8eaf3d1bb363dd05987c077b16d2af7f36ee..e30bb5a312f9b3088f660a7f5036b0504f21dc98 100755
--- a/.travis/install.xdrfile
+++ b/.travis/install.xdrfile
@@ -3,7 +3,7 @@
set -e
set -x
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
echo "installing xdrfile library"
# wget ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
diff --git a/CHANGES/v2.3.md b/CHANGES/v2.3.md
index 4992933394d233af87c82e1a515a0f883f661c8b..fbe3446704f5a86656f15e556d7f842c4aed1e0e 100644
--- a/CHANGES/v2.3.md
+++ b/CHANGES/v2.3.md
@@ -201,13 +201,29 @@ For developers:
find them without explicitly setting `DYLD_LIBRARY_PATH`. This should also make the `DYLD_LIBRARY_PATH` irrelevant.
Notice that `DYLD_LIBRARY_PATH` is not well behaved in OSX El Capitan.
-## Version 2.3.4 (unreleased)
+## Version 2.3.4 (Dec 15, 2017)
For users:
-- GROMACS patch updated to gromacs-2016.4
+- GROMACS patch updated to gromacs-2016.4. This patch was also fixed in order to properly work with \ref ENERGY (see \issue{316})
+ and to implement `-hrex` option (see \issue{197}).
+- Patch for GROMACS 5.1.4 updated to fix an error with \ref ENERGY (see \issue{316}).
+- Solved a bug in \ref ERMSD leading to incorrect results when using non-default length units (e.g. with `UNITS LENGTH=A`).
For developers:
- Regtest script also reports when exitcode different from zero is returned.
+- Patch script reports errors returning a nonzero exit code.
- cppcheck update to 1.81
+- Solved small bug in stored PLUMED_ROOT directory as obtained from statically patched MD codes.
+ Namely, the compilation directory was stored rather than the installation one.
+
+## Version 2.3.5
+
+For users:
+- Fixed `plumed partial_tempering` to agree with GROMACS conventions for choice of dihedrals (see \issue{337}).
+ Should be irrelevant for the vast majority of cases.
+
+For developers:
+- Doxygen on travis-ci has been updated to 1.8.14
+- `make clean` now correctly removes the `src/lib/plumed` executable.
diff --git a/CHANGES/v2.4.md b/CHANGES/v2.4.md
index bd96c721fdfaadff1d3fd572e4071018fa9afdc1..f70f6fdfed054542a9c8006ab9638c64d7ef1939 100644
--- a/CHANGES/v2.4.md
+++ b/CHANGES/v2.4.md
@@ -1,6 +1,6 @@
@page CHANGES-2-4 Version 2.4
-## Version 2.4b (Oct 3, 2017)
+## Version 2.4 (Dec 15, 2017)
Version 2.4 contains several improvements with respect to 2.3. Users currently working with 2.3
should have a look at the section "Changes leading to incompatible behavior" below and
@@ -113,8 +113,10 @@ Changes from version 2.3 which are relevant for users:
- \ref PATHMSD and \ref PROPERTYMAP now support alignment to a close structure (thanks to Jana Pazurikova)
- PDB files with more than 100k atoms can now be read using [hybrid 36](http://cci.lbl.gov/hybrid_36/) format,
see \issue{226}.
- - Added experimental lepton support. Set env var `export PLUMED_USE_LEPTON=yes` to activate lepton as a matheval replacement.
- Notice that this is an experimental feature and is not fully validated yet. See \issue{244}.
+ - Added lepton support. Set env var `export PLUMED_USE_LEPTON=yes` to activate lepton as a matheval replacement
+ in \ref MATHEVAL, \ref CUSTOM, and \ref switchingfunction "MATHEVAL switching function".
+ Notice that in v2.5 matheval support will be dropped and all these keywords will use lepton.
+ See \issue{244}.
- When parsing constants, PLUMED uses lepton library. This allows to pass
arguments such as `HEIGHT=exp(0.5)` (see \ref parsing-constants).
- \ref CUSTOM function has been added as an alias to \ref MATHEVAL .
@@ -125,7 +127,10 @@ Changes from version 2.3 which are relevant for users:
- Examples in the documentation now have syntax highlighting and links to the documentation of used actions.
- \ref COORDINATIONNUMBER : Added option to have pairwise distance moments of coordination number in the multicolvar module
- GROMACS patch updated to gromacs-2016.4
+ - Implemented HREX for gromacs-2016.4.
+ - Added patch for Quantum ESPRESSO 6.2 (thanks to Ralf Meyer).
- Fixed a bug in \ref LOCAL_AVERAGE which appears when you use SPECIESA and SPECIESB keywords instead of just SPECIES
+ - Added possibility to pass `--kt` from \ref driver.
Changes from version 2.3 which are relevant for developers:
- A few fixes has been made to improve exception safety. Although we still cannot declare
@@ -135,6 +140,7 @@ Changes from version 2.3 which are relevant for developers:
- Due to the required c++11 support, travis-ci test on Ubuntu Precise has been removed.
- `gettimeofdate` and `gettime` have been replaced with portable `chrono` classes introduced in c++11.
- C++ exceptions are enabled by default.
+ - A large number of loops have been changed to use the `auto` keyword in order to improve code readability.
- Stack trace is not written upon error anymore, unless environment variable `PLUMED_STACK_TRACE` is set at runtime.
- Fixed a potential bug using single precision system blas on a mac (notice that currently plumed only uses
double precision, so it is harmless).
@@ -146,14 +152,18 @@ Changes from version 2.3 which are relevant for developers:
- environment variable `LDSO` has been renamed to `LDSHARED`, which is standard in the python community.
- a `libplumedWrapper.a` library is installed as well, that is used in `--runtime` patching.
- pkgconfig files are installed.
-
-Fixes after beta release:
- - Fixed a bug in EDS module for restarts, where accumulated rate was not stored to restart file, leading to convergence problems.
- - (developers) `plumed config makefile_conf` can be used to retrieve `Makefile.conf` file a posteriori.
- - Added patch for Quantum ESPRESSO 6.2 (thanks to Ralf Meyer).
- - (developers) Store `MPIEXEC` variable at configure time and use it later for running regtests. Notice that in case
+ - `plumed config makefile_conf` can be used to retrieve `Makefile.conf` file a posteriori.
+ - Store `MPIEXEC` variable at configure time and use it later for running regtests. Notice that in case
`MPIEXEC` is not specified regtests will be run using the command stored in env var `PLUMED_MPIRUN` or, if this is
also not defined, using `mpirun`.
- - (developers) Added canonical makefile targets `check` and `installcheck`. Notice that `check` runs checks with
+ - Added canonical makefile targets `check` and `installcheck`. Notice that `check` runs checks with
non-installed plumed whereas `installcheck` uses the installed one, including its correct program name if it
was personalized (e.g. with suffixes). Notice that this modifies the previously available `check` target.
+
+
+## Version 2.4.1
+
+For users:
+ - Resolved a problem with \ref CS2BACKBONE and glycine atom names.
+ - Module VES: Fixed a bug with basis functions that have a constant function different from 1 (e.g. scaled version of the Legendre basis functions, \ref BF_LEGENDRE) that was causing a time-dependent shift in the bias potential.
+ - Module VES: In optimizers (\ref OPT_AVERAGED_SGD and \ref OPT_DUMMY) the output of quantities related to the instantaneous gradients are now off by default as these quantities are generally not useful for normal users, their output can instead by re-enabled by using the MONITOR_INSTANTANEOUS_GRADIENT keyword. Also added an keyword MONITOR_AVERAGE_GRADIENT that allows to monitor the averged gradient and output quantities related to it.
diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md
index 7307c24b1888bd85e14a7e482a7922669cc40459..c4f9f381946785c296ba6172ff40fa7c3feaecf4 100644
--- a/CHANGES/v2.5.md
+++ b/CHANGES/v2.5.md
@@ -4,15 +4,25 @@ This page contains changes that will end up in 2.5
Changes from version 2.4 which are relevant for users:
- Changes leading to incompatible behavior:
+
- New actions:
- \ref PAMM
- \ref HBPAMM_MATRIX
- \ref HBPAMM_SH
-- Libmatheval is not used anymore. \ref MATHEVAL (and \ref CUSTOM) are still available
- but employ an internal implementation of the lepton library. There should be no observable difference
- except from the fact that lepton does not support some of the inverse and hyperbolic functions supported
- by matheval (easily writable as a function of the available ones).
+
+- Other changes:
+ - \ref EXTERNAL can now SCALE the input grid. This allows for more flexibility without modifying the grid file.
+ - \ref ALPHABETA can now combine dihedrals with different coefficients
+ - \ref CS2BACKBONE (isdb module) is now mpi parallelised in particular with DOSCORE and CAMSHIFT
+ - Libmatheval is not used anymore. \ref MATHEVAL (and \ref CUSTOM) are still available
+ but employ an internal implementation of the lepton library. There should be no observable difference
+ except from the fact that lepton does not support some of the inverse and hyperbolic functions supported
+ by matheval (easily writable as a function of the available ones).
Changes from version 2.4 which are relevant for developers:
- Code has been cleanup up replacing a number of pointers with `std::unique_ptr`.
(WORK IN PROGRESS: in principle we could aim at eliminating all delete statements)
+- Exceptions cannot be disabled (`--disable-cxx-exceptions` option has been removed from `./configure`.
+- Every exception thrown in PLUMED now also writes its message on PLUMED log.
+- On OSX, `libplumed.dylib` links to `libplumedKernel.dylib` and `plumed` links to `libplumed.dylib`.
+
diff --git a/README.md b/README.md
index c5cd4aa1c825000c4265e4fb545683cdebf2ef4c..16c6fe2693d35ac3111a8a132d62eaedd47c55f4 100644
--- a/README.md
+++ b/README.md
@@ -38,14 +38,14 @@ Status
Below you find the status on [Travis-CI](http://travis-ci.org/plumed/plumed2) for the release branches.
-| Branch | Status | First stable release | Still supported |
+| Branch | Status | First stable release (year) | Still supported |
|:--------:|:-------------:|:--------:|:------:|
-| master | [](https://travis-ci.org/plumed/plumed2) | v2.5.0 is expected late 2018 | / |
-| v2.4 | [](https://travis-ci.org/plumed/plumed2) | v2.4.0 is expected late 2017 | yes |
-| v2.3 | [](https://travis-ci.org/plumed/plumed2) | Dec 12, 2016 | yes |
-| v2.2 | [](https://travis-ci.org/plumed/plumed2) | Oct 13, 2015 |no |
-| v2.1 | [](https://travis-ci.org/plumed/plumed2) | Sep 9, 2014 | no |
-| v2.0 | Not available | Sep 27, 2013 | no |
+| master | [](https://travis-ci.org/plumed/plumed2) | 2018 (expected) | / |
+| v2.4 | [](https://travis-ci.org/plumed/plumed2) | 2017 | yes |
+| v2.3 | [](https://travis-ci.org/plumed/plumed2) | 2016 | yes |
+| v2.2 | [](https://travis-ci.org/plumed/plumed2) | 2015 |no |
+| v2.1 | [](https://travis-ci.org/plumed/plumed2) | 2014 | no |
+| v2.0 | Not available | 2013 | no |
Content
-------
diff --git a/configure b/configure
index bb24ab85bff57f3f8ad7b0fd97037ffcd105c79a..6318dc34312f579c864f118903b4c12aa918114c 100755
--- a/configure
+++ b/configure
@@ -710,7 +710,6 @@ enable_debug_glibcxx
enable_shared
enable_dependency_tracking
enable_rpath
-enable_cxx_exceptions
enable_ld_r
enable_ar_cr
enable_mpi
@@ -1379,7 +1378,6 @@ Optional Features:
--enable-dependency-tracking
enable dependency tracking, default: yes
--enable-rpath enable store rpath, default: no
- --enable-cxx-exceptions enable c++ exceptions, default: yes
--enable-ld-r enable group object files, default: yes
--enable-ar-cr enable use ar to build libplumedWrapper.a, default:
yes
@@ -2671,24 +2669,6 @@ fi
-cxx_exceptions=
-# Check whether --enable-cxx-exceptions was given.
-if test "${enable_cxx_exceptions+set}" = set; then :
- enableval=$enable_cxx_exceptions; case "${enableval}" in
- (yes) cxx_exceptions=true ;;
- (no) cxx_exceptions=false ;;
- (*) as_fn_error $? "wrong argument to --enable-cxx-exceptions" "$LINENO" 5 ;;
- esac
-else
- case "yes" in
- (yes) cxx_exceptions=true ;;
- (no) cxx_exceptions=false ;;
- esac
-
-fi
-
-
-
ld_r=
# Check whether --enable-ld-r was given.
if test "${enable_ld_r+set}" = set; then :
@@ -8298,13 +8278,6 @@ $as_echo "$as_me: Check boundaries, adding -D_GLIBCXX_DEBUG" >&6;}
fi
-if test "$cxx_exceptions" == true ; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: Enabling c++ exceptions -D__PLUMED_HAS_EXCEPTIONS" >&5
-$as_echo "$as_me: Enabling c++ exceptions -D__PLUMED_HAS_EXCEPTIONS" >&6;}
- $as_echo "#define __PLUMED_HAS_EXCEPTIONS 1" >>confdefs.h
-
-fi
-
# this is necessary in many MPI implementations
# I leave it by default, since it seems harmless
$as_echo "#define _REENTRANT 1" >>confdefs.h
diff --git a/configure.ac b/configure.ac
index 5a5353cf8c19519c6171f00c40792ece6c1b1640..9e67e4ec851c815b56d7de7d41db22e970ea7d19 100644
--- a/configure.ac
+++ b/configure.ac
@@ -237,7 +237,6 @@ PLUMED_CONFIG_ENABLE([debug-glibcxx],[enable boundary check],[no])
PLUMED_CONFIG_ENABLE([shared],[shared libs],[yes])
PLUMED_CONFIG_ENABLE([dependency-tracking],[dependency tracking],[yes])
PLUMED_CONFIG_ENABLE([rpath],[store rpath],[no])
-PLUMED_CONFIG_ENABLE([cxx-exceptions],[c++ exceptions],[yes])
PLUMED_CONFIG_ENABLE([ld-r],[group object files],[yes])
PLUMED_CONFIG_ENABLE([ar-cr],[use ar to build libplumedWrapper.a],[yes])
PLUMED_CONFIG_ENABLE([mpi],[search for mpi],[yes])
@@ -687,11 +686,6 @@ if test "$debug_glibcxx" == true ; then
AC_DEFINE([_GLIBCXX_DEBUG])
fi
-if test "$cxx_exceptions" == true ; then
- AC_MSG_NOTICE([Enabling c++ exceptions -D__PLUMED_HAS_EXCEPTIONS])
- AC_DEFINE([__PLUMED_HAS_EXCEPTIONS])
-fi
-
# this is necessary in many MPI implementations
# I leave it by default, since it seems harmless
AC_DEFINE([_REENTRANT])
diff --git a/developer-doc/plmdIntro.md b/developer-doc/plmdIntro.md
index c9a0a0434cf064f507d234351c50750a2058e1bb..c66bbd7e43d89f2007dcf96a8bb15ed16f9f9217 100644
--- a/developer-doc/plmdIntro.md
+++ b/developer-doc/plmdIntro.md
@@ -503,9 +503,13 @@ unique_ptr in advance, you should insert it with the following syntax
Notice that also forward declarations discussed above are a bit simpler
to implement using C++11 syntax. This can be done using a std::unique_ptr
-or, even better, using the class ForwardDecl, which is similar to
-a std::unique_ptr but only implements the necessary method in order to be
-less error prone.
+or, even better, using the class ForwardDecl, which is a small utility class that
+only implement two methods:
+- A constructor, which takes an arbitrary number of parameters and use them
+ to construct an internally stored `std::unique_ptr`.
+- A `operator *`, which returns a pointer to the object.
+
+An example usage is below:
\verbatim
@@ -540,8 +544,8 @@ public:
using namespace PLMD;
B::B():
- content1_fwd(*new A),
- content2_fwd(*new A (argument))
+// constructors that need no argument can be omitted
+ content2_fwd(argument)
{
}
diff --git a/macports/Portfile.in b/macports/Portfile.in
index b3ceeae7a283fbedfc9c4e89aa951932c05d86a5..a923394d348da33cb2600566d4a3e68c227351de 100644
--- a/macports/Portfile.in
+++ b/macports/Portfile.in
@@ -83,7 +83,7 @@ depends_lib-append port:xdrfile port:zlib port:gsl
# Notice that one of the optional modules (drr) requires boost_serialization
variant allmodules description {Enable all optional modules} {
configure.args-append --enable-modules=all --enable-boost-serialization
- configure.ldflags-append -lboost_serialization
+ configure.ldflags-append -lboost_serialization-mt
depends_lib-append port:boost
}
@@ -95,3 +95,8 @@ pre-configure {
configure.ldflags-append ${linalglib}
}
+# Allow running tests from MacPorts
+test.run yes
+test.target check
+
+
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp b/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
index f3b5243851f1d5ec8364577677bae9404b270fc7..b6e0fd4d42078a4e6c819440a13a45ffe28c9ee6 100644
--- a/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/md.cpp
@@ -127,6 +127,10 @@ extern int plumedswitch;
extern plumed plumedmain;
/* END PLUMED */
+/* PLUMED HREX */
+extern int plumed_hrex;
+/* END PLUMED HREX */
+
#ifdef GMX_FAHCORE
#include "corewrap.h"
#endif
@@ -727,8 +731,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
plumed_cmd(plumedmain,"setMDEngine","gromacs");
plumed_cmd(plumedmain,"setLog",fplog);
- real real_delta_t;
- real_delta_t=ir->delta_t;
+ real real_delta_t=ir->delta_t;
plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
plumed_cmd(plumedmain,"init",NULL);
@@ -1087,6 +1090,91 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
}
clear_mat(force_vir);
+ /* PLUMED HREX */
+ gmx_bool bHREX = bDoReplEx && plumed_hrex;
+
+ if (plumedswitch && bHREX) {
+ gmx_enerdata_t *hrex_enerd;
+ snew(hrex_enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr,ir->fepvals->n_lambda,hrex_enerd);
+ int repl = -1;
+ int nrepl = -1;
+ if (MASTER(cr)){
+ repl = replica_exchange_get_repl(repl_ex);
+ nrepl = replica_exchange_get_nrepl(repl_ex);
+ }
+
+ if (DOMAINDECOMP(cr)) {
+ dd_collect_state(cr->dd,state,state_global);
+ } else {
+ copy_state_nonatomdata(state, state_global);
+ }
+
+ if(MASTER(cr)){
+ if(repl%2==step/repl_ex_nst%2){
+ if(repl-1>=0) exchange_state(cr->ms,repl-1,state_global);
+ }else{
+ if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
+ }
+ }
+ if (!DOMAINDECOMP(cr)) {
+ copy_state_nonatomdata(state_global, state);
+ }
+ if(PAR(cr)){
+ if (DOMAINDECOMP(cr)) {
+ dd_partition_system(fplog,step,cr,TRUE,1,
+ state_global,top_global,ir,
+ state,&f,mdatoms,top,fr,vsite,constr,
+ nrnb,wcycle,FALSE);
+ }
+ }
+ do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
+ state->box, state->x, &state->hist,
+ f, force_vir, mdatoms, hrex_enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
+ GMX_FORCE_STATECHANGED |
+ GMX_FORCE_DYNAMICBOX |
+ GMX_FORCE_ALLFORCES |
+ GMX_FORCE_VIRIAL |
+ GMX_FORCE_ENERGY |
+ GMX_FORCE_DHDL |
+ GMX_FORCE_NS);
+
+ plumed_cmd(plumedmain,"GREX cacheLocalUSwap",&hrex_enerd->term[F_EPOT]);
+ sfree(hrex_enerd);
+
+ /* exchange back */
+ if (DOMAINDECOMP(cr)) {
+ dd_collect_state(cr->dd,state,state_global);
+ } else {
+ copy_state_nonatomdata(state, state_global);
+ }
+
+ if(MASTER(cr)){
+ if(repl%2==step/repl_ex_nst%2){
+ if(repl-1>=0) exchange_state(cr->ms,repl-1,state_global);
+ }else{
+ if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
+ }
+ }
+
+ if (!DOMAINDECOMP(cr)) {
+ copy_state_nonatomdata(state_global, state);
+ }
+ if(PAR(cr)){
+ if (DOMAINDECOMP(cr)) {
+ dd_partition_system(fplog,step,cr,TRUE,1,
+ state_global,top_global,ir,
+ state,&f,mdatoms,top,fr,vsite,constr,
+ nrnb,wcycle,FALSE);
+ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
+ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
+ }
+ }
+ }
+ /* END PLUMED HREX */
+
/* We write a checkpoint at this MD step when:
* either at an NS step when we signalled through gs,
* or at the last step (but not when we do not want confout),
@@ -1179,6 +1267,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if(pversion>3) plumed_cmd(plumedmain,"doCheckPoint",&checkp);
plumed_cmd(plumedmain,"setForces",&f[0][0]);
plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+ if(plumedNeedsEnergy) force_flags |= GMX_FORCE_ENERGY | GMX_FORCE_VIRIAL;
clear_mat(plumed_vir);
plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
}
@@ -1200,9 +1289,9 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
msmul(plumed_vir,0.5,plumed_vir);
m_add(force_vir,plumed_vir,force_vir);
}
- if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
- do_per_step(step,repl_ex_nst)) plumed_cmd(plumedmain,"GREX savePositions",NULL);
+ if(bDoReplEx) plumed_cmd(plumedmain,"GREX savePositions",NULL);
if(plumedWantsToStop) ir->nsteps=step_rel+1;
+ if(bHREX) plumed_cmd(plumedmain,"GREX cacheLocalUNow",&enerd->term[F_EPOT]);
}
/* END PLUMED */
}
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp
index cf0f72cf87e0d872581031f270cc4facc600212d..2b131b65dec2c57bc7d7eb6271da9cd67d509a4f 100644
--- a/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/mdrun.cpp
@@ -78,6 +78,10 @@ extern plumed plumedmain;
extern void(*plumedcmd)(plumed,const char*,const void*);
/* END PLUMED */
+/* PLUMED HREX */
+int plumed_hrex;
+/* END PLUMED HREX */
+
/*! \brief Return whether either of the command-line parameters that
* will trigger a multi-simulation is set */
static bool is_multisim_option_set(int argc, const char *const argv[])
@@ -403,6 +407,8 @@ int gmx_mdrun(int argc, char *argv[])
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
+ { "-hrex", FALSE, etBOOL, {&plumed_hrex},
+ "Enable hamiltonian replica exchange" },
{ "-imdport", FALSE, etINT, {&imdport},
"HIDDENIMD listening port" },
{ "-imdwait", FALSE, etBOOL, {&bIMDwait},
@@ -571,6 +577,15 @@ int gmx_mdrun(int argc, char *argv[])
plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
plumedswitch=1;
}
+ /* PLUMED HREX*/
+ if(getenv("PLUMED_HREX")) plumed_hrex=1;
+ if(plumed_hrex){
+ if(!plumedswitch) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) requires -plumed");
+ if(repl_ex_nst==0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) replica exchange");
+ if(repl_ex_nex!=0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) not compatible with -nex");
+ }
+ /* END PLUMED HREX */
+
/* END PLUMED */
rc = gmx::mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose,
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp
index 70d9f30b8d2b0194a2e2ab77fcae34e1b6e679a8..a7165fcac686d4de362a3c9ff914b62f18c97889 100644
--- a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.cpp
@@ -67,6 +67,10 @@ extern int plumedswitch;
extern plumed plumedmain;
/* END PLUMED */
+/* PLUMED HREX */
+extern int plumed_hrex;
+/* END PLUMED HREX */
+
#define PROBABILITYCUTOFF 100
/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
@@ -543,7 +547,9 @@ static void exchange_rvecs(const gmx_multisim_t gmx_unused *ms, int gmx_unused b
}
}
-static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
+/* PLUMED HREX */
+void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
+/* END PLUMED HREX */
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
@@ -623,7 +629,9 @@ static void copy_ints(const int *s, int *d, int n)
#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
#define scopy_ints(v, n) copy_ints(state->v, state_local->v, n);
-static void copy_state_nonatomdata(t_state *state, t_state *state_local)
+/* PLUMED HREX */
+void copy_state_nonatomdata(t_state *state, t_state *state_local)
+/* END PLUMED HREX */
{
/* When t_state changes, this code should be updated. */
int ngtc, nnhpres;
@@ -866,6 +874,11 @@ static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int
{
fprintf(fplog, "Repl %d <-> %d dE_term = %10.3e (kT)\n", a, b, delta);
}
+/* PLUMED HREX */
+/* this is necessary because with plumed HREX the energy contribution is
+ already taken into account */
+ if(plumed_hrex) delta=0.0;
+/* END PLUMED HREX */
if (re->bNPT)
{
/* revist the calculation for 5.0. Might be some improvements. */
@@ -980,6 +993,7 @@ test_for_replica_exchange(FILE *fplog,
/* PLUMED */
int plumed_test_exchange_pattern=0;
+ if(plumed_test_exchange_pattern && plumed_hrex) gmx_fatal(FARGS,"hrex not compatible with ad hoc exchange patterns");
/* END PLUMED */
if (bMultiEx)
@@ -1488,3 +1502,15 @@ void print_replica_exchange_statistics(FILE *fplog, struct gmx_repl_ex *re)
/* print the transition matrix */
print_transition_matrix(fplog, re->nrepl, re->nmoves, re->nattempt);
}
+
+/* PLUMED HREX */
+int replica_exchange_get_repl(const gmx_repl_ex_t re){
+ return re->repl;
+};
+
+int replica_exchange_get_nrepl(const gmx_repl_ex_t re){
+ return re->nrepl;
+};
+/* END PLUMED HREX */
+
+
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h
new file mode 100644
index 0000000000000000000000000000000000000000..32499012ad3e086bb60a980a3d9b67bf547fd851
--- /dev/null
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h
@@ -0,0 +1,87 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef _repl_ex_h
+#define _repl_ex_h
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+struct t_state;
+
+/* Abstract type for replica exchange */
+typedef struct gmx_repl_ex *gmx_repl_ex_t;
+
+gmx_repl_ex_t init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ int nst, int nmultiex, int init_seed);
+/* Should only be called on the master nodes */
+
+gmx_bool replica_exchange(FILE *fplog,
+ const t_commrec *cr,
+ gmx_repl_ex_t re,
+ t_state *state, gmx_enerdata_t *enerd,
+ t_state *state_local,
+ gmx_int64_t step, real time);
+/* Attempts replica exchange, should be called on all nodes.
+ * Returns TRUE if this state has been exchanged.
+ * When running each replica in parallel,
+ * this routine collects the state on the master node before exchange.
+ * With domain decomposition, the global state after exchange is stored
+ * in state and still needs to be redistributed over the nodes.
+ */
+
+void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
+/* Should only be called on the master nodes */
+
+/* PLUMED HREX */
+extern int replica_exchange_get_repl(const gmx_repl_ex_t re);
+extern int replica_exchange_get_nrepl(const gmx_repl_ex_t re);
+extern void pd_collect_state(const t_commrec *cr, t_state *state);
+extern void exchange_state(const gmx_multisim_t *ms, int b, t_state *state);
+extern void copy_state_nonatomdata(t_state *state, t_state *state_local);
+/* END PLUMED HREX */
+
+#endif /* _repl_ex_h */
diff --git a/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed
new file mode 100644
index 0000000000000000000000000000000000000000..dcb47d1fdd3a425bdb4f1414c259bddff07ac653
--- /dev/null
+++ b/patches/gromacs-2016.4.diff/src/programs/mdrun/repl_ex.h.preplumed
@@ -0,0 +1,79 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef _repl_ex_h
+#define _repl_ex_h
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+struct t_state;
+
+/* Abstract type for replica exchange */
+typedef struct gmx_repl_ex *gmx_repl_ex_t;
+
+gmx_repl_ex_t init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ int nst, int nmultiex, int init_seed);
+/* Should only be called on the master nodes */
+
+gmx_bool replica_exchange(FILE *fplog,
+ const t_commrec *cr,
+ gmx_repl_ex_t re,
+ t_state *state, gmx_enerdata_t *enerd,
+ t_state *state_local,
+ gmx_int64_t step, real time);
+/* Attempts replica exchange, should be called on all nodes.
+ * Returns TRUE if this state has been exchanged.
+ * When running each replica in parallel,
+ * this routine collects the state on the master node before exchange.
+ * With domain decomposition, the global state after exchange is stored
+ * in state and still needs to be redistributed over the nodes.
+ */
+
+void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
+/* Should only be called on the master nodes */
+
+#endif /* _repl_ex_h */
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp b/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp
index 1e2c620ea83406026c17e6e10ec25f80b880ba70..d4bb5960fb564e760c7372ebb56cce5d280a3cd2 100644
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp
+++ b/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp
@@ -1055,7 +1055,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
/* PLUMED HREX */
gmx_bool bHREX;
- bHREX= repl_ex_nst > 0 && (step>0) && !bLastStep && do_per_step(step,repl_ex_nst) && plumed_hrex;
+ bHREX = bDoReplEx && plumed_hrex;
if(plumedswitch) if(bHREX){
gmx_enerdata_t *hrex_enerd;
@@ -1249,6 +1249,7 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
if(pversion>3) plumed_cmd(plumedmain,"doCheckPoint",&checkp);
plumed_cmd(plumedmain,"setForces",&f[0][0]);
plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
+ if(plumedNeedsEnergy) force_flags |= (GMX_FORCE_ENERGY | GMX_FORCE_VIRIAL);
clear_mat(plumed_vir);
plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
}
@@ -1270,11 +1271,9 @@ double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
msmul(plumed_vir,0.5,plumed_vir);
m_add(force_vir,plumed_vir,force_vir);
}
- if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
- do_per_step(step,repl_ex_nst)) plumed_cmd(plumedmain,"GREX savePositions",NULL);
+ if(bDoReplEx) plumed_cmd(plumedmain,"GREX savePositions",NULL);
if(plumedWantsToStop) ir->nsteps=step_rel+1;
- if(bHREX)
- plumed_cmd(plumedmain,"GREX cacheLocalUNow",&enerd->term[F_EPOT]);
+ if(bHREX) plumed_cmd(plumedmain,"GREX cacheLocalUNow",&enerd->term[F_EPOT]);
}
/* END PLUMED */
}
diff --git a/patches/patch.sh b/patches/patch.sh
index f198d8dfb9b4e10bb00d3dba291404a2119e5ddb..ece5948d89179e01d92dca299901fc57196be48a 100755
--- a/patches/patch.sh
+++ b/patches/patch.sh
@@ -90,20 +90,20 @@ do
(--quiet|-q) quiet=yes ;;
(*)
echo "ERROR: Unknown option $prefix_option. Use -h for help."
- exit
+ exit 1
esac
done
if [ -n "$mdroot" ] ; then
if ! cd "$mdroot" ; then
- echo "Directory $mdroot does not exist"
- exit
+ echo "ERROR: Directory $mdroot does not exist"
+ exit 1
fi
fi
if [ -n "$multiple_actions" ] ; then
- echo "Too many actions. -h for help"
- exit
+ echo "ERROR: Too many actions. -h for help"
+ exit 1
fi
if [ -z "$action" ] ; then
@@ -117,13 +117,13 @@ if [ -z "$PLUMED_ROOT" ]
then
echo "ERROR: I cannot find PLUMED"
echo "Please set PLUMED_ROOT environment variable or use --root"
- exit
+ exit 1
fi
if [ ! -d "$PLUMED_ROOT/patches/" ]
then
echo "ERROR: cannot find $PLUMED_ROOT/patches/ directory"
echo "Check your PLUMED_ROOT variable or --root option"
- exit
+ exit 1
fi
# build MD engines list
@@ -153,7 +153,7 @@ then
test -n "$quiet" || echo "Creating a new patch"
if [[ -e "$PLUMED_ROOT"/patches/"$newpatch".diff ]] ; then
echo "ERROR: patch $newpatch is already defined"
- exit
+ exit 1
fi
touch "$PLUMED_ROOT"/patches/"$newpatch".diff
test -n "$quiet" || echo "Created file $PLUMED_ROOT/patches/$newpatch.diff"
@@ -204,8 +204,8 @@ fi
case "$mode" in
(static|shared|runtime) ;;
(*)
- echo "I don't understand mode $mode"
- exit
+ echo "ERROR: I don't understand mode $mode"
+ exit 1
esac
@@ -213,7 +213,7 @@ case "$action" in
(patch)
if [ ! -e "$diff" ] ; then
echo "ERROR: MD engine not supported (or mispelled)"
- exit
+ exit 1
fi
if type -t plumed_preliminary_test 1>/dev/null ; then
if plumed_preliminary_test || [ "$force" ] ; then
@@ -222,25 +222,25 @@ case "$action" in
echo "ERROR: Preliminary test not passed."
echo "It seems that this is not $engine, or you are in the wrong directory"
echo "If you are sure about what you are doing, use -f"
- exit
+ exit 1
fi
fi
if [ -L Plumed.h -o -L Plumed.inc ]
then
echo "ERROR: you have likely already patched. Revert first (-r)"
- exit
+ exit 1
fi
if [ ! -f "$PLUMED_ROOT/src/lib/Plumed.inc" ]
then
echo "ERROR: cannot find $PLUMED_ROOT/src/lib/Plumed.inc file"
echo "Compile plumed before patching"
- exit
+ exit 1
fi
if [ ! -f "$PLUMED_ROOT/src/lib/Plumed.cmake.$mode" ]
then
echo "ERROR: cannot find $PLUMED_ROOT/src/lib/Plumed.cmake.$mode file"
echo "Compile a $mode version of plumed before patching, or change patching mode [static|shared|runtime]"
- exit
+ exit 1
fi
if type -t plumed_before_patch 1>/dev/null ; then
test -n "$quiet" || echo "Executing plumed_before_patch function"
@@ -307,12 +307,12 @@ case "$action" in
if [ ! -L Plumed.h -o ! -L Plumed.inc ]
then
echo "ERROR: I cannot find Plumed.h and Plumed.inc files. You have likely not patched yet."
- exit
+ exit 1
fi
PREPLUMED=$(find . -name "*.preplumed" | sort)
if ! test "$PREPLUMED" ; then
echo "ERROR: I cannot find any .preplumed file. There is nothing to save."
- exit
+ exit 1
fi
if type -t plumed_preliminary_test 1>/dev/null ; then
if plumed_preliminary_test || [ "$force" ] ; then
@@ -321,7 +321,7 @@ case "$action" in
echo "ERROR: Preliminary test not passed."
echo "It seems that this is not $engine, or you are in the wrong directory"
echo "If you are sure about what you are doing, use -f"
- exit
+ exit 1
fi
fi
test -n "$quiet" || echo "Saving your changes to $diff"
@@ -378,7 +378,7 @@ EOF
(revert)
if [ ! -e "$diff" ] ; then
echo "ERROR: MD engine not supported (or mispelled)"
- exit
+ exit 1
fi
if type -t plumed_before_revert 1>/dev/null ; then
test -n "$quiet" || echo "Executing plumed_before_revert function"
diff --git a/regtest/basic/rt-ermsd2/Makefile b/regtest/basic/rt-ermsd2/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt-ermsd2/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt-ermsd2/colvar.reference b/regtest/basic/rt-ermsd2/colvar.reference
new file mode 100644
index 0000000000000000000000000000000000000000..86cf3d0b1fe1a45bbea876efaf86f0114f443f39
--- /dev/null
+++ b/regtest/basic/rt-ermsd2/colvar.reference
@@ -0,0 +1,11 @@
+#! FIELDS time e e2
+ 0.000000 0.00078 0.00000
+ 1.000000 0.61839 0.10157
+ 2.000000 0.58178 0.08616
+ 3.000000 0.83629 0.09939
+ 4.000000 0.79844 0.11675
+ 5.000000 0.82803 0.10357
+ 6.000000 0.87762 0.10627
+ 7.000000 0.79849 0.06094
+ 8.000000 0.90058 0.11108
+ 9.000000 1.02312 0.04906
diff --git a/regtest/basic/rt-ermsd2/config b/regtest/basic/rt-ermsd2/config
new file mode 100644
index 0000000000000000000000000000000000000000..03781ec82a643e2776b9b69254e7e336e0293fc7
--- /dev/null
+++ b/regtest/basic/rt-ermsd2/config
@@ -0,0 +1,6 @@
+type=driver
+# this is to test a different name
+#arg="--plumed plumed.dat --mf_xtc samples.xtc"
+#arg="--plumed plumed.dat --igro broken.gro"
+#arg="--plumed plumed.dat --igro before.gro"
+arg="--plumed plumed.dat --mf_xtc traj.xtc"
diff --git a/regtest/basic/rt-ermsd2/der.reference b/regtest/basic/rt-ermsd2/der.reference
new file mode 100644
index 0000000000000000000000000000000000000000..5ceb7d1085183bada00fc3a286cab4673fc1f06c
--- /dev/null
+++ b/regtest/basic/rt-ermsd2/der.reference
@@ -0,0 +1,6481 @@
+#! FIELDS time parameter e e2
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diff --git a/regtest/basic/rt-ermsd2/plumed.dat b/regtest/basic/rt-ermsd2/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..a0025185222810deb50653f60ba35d9f17d7e61a
--- /dev/null
+++ b/regtest/basic/rt-ermsd2/plumed.dat
@@ -0,0 +1,18 @@
+UNITS LENGTH=A
+MOLINFO STRUCTURE=ref.pdb
+
+e: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb
+
+e2: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb PAIRS=1,2,1,3,1,4,2,3,2,4,3,4
+
+DUMPDERIVATIVES ARG=e,e2 FILE=der FMT=%9.3f
+
+PRINT ARG=e,e2 FILE=colvar FMT=%9.5f
+
+# ne: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb NUMERICAL_DERIVATIVES
+
+# ne2: ERMSD ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6,@lcs-7,@lcs-8,@lcs-9,@lcs-10,@lcs-11,@lcs-12,@lcs-13,@lcs-14,@lcs-15,@lcs-16,@lcs-17,@lcs-18,@lcs-19,@lcs-20,@lcs-21,@lcs-22,@lcs-23,@lcs-24,@lcs-25,@lcs-26,@lcs-27,@lcs-28,@lcs-29,@lcs-30,@lcs-31,@lcs-32,@lcs-33,@lcs-34,@lcs-35,@lcs-36,@lcs-37,@lcs-38,@lcs-39,@lcs-40,@lcs-41,@lcs-42,@lcs-43,@lcs-44,@lcs-45,@lcs-46,@lcs-47,@lcs-48,@lcs-49,@lcs-50,@lcs-51,@lcs-52,@lcs-53,@lcs-54,@lcs-55,@lcs-56,@lcs-57,@lcs-58,@lcs-59,@lcs-60,@lcs-61,@lcs-62,@lcs-63,@lcs-64,@lcs-65,@lcs-66,@lcs-67,@lcs-68,@lcs-69,@lcs-70,@lcs-71 REFERENCE=ref.pdb PAIRS=1,2,1,3,1,4,2,3,2,4,3,4 NUMERICAL_DERIVATIVES
+
+# DUMPDERIVATIVES ARG=e,ne FILE=nder
+
+
diff --git a/regtest/basic/rt-ermsd2/ref.pdb b/regtest/basic/rt-ermsd2/ref.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..a2da33b61b9a0bbf7aad7db7fead1c4bf3174811
--- /dev/null
+++ b/regtest/basic/rt-ermsd2/ref.pdb
@@ -0,0 +1,2264 @@
+REMARK GENERATED BY TRJCONV
+TITLE add Villa in water t= 0.00000
+REMARK THIS IS A SIMULATION BOX
+CRYST1 79.904 79.904 79.904 60.00 60.00 90.00 P 1 1
+MODEL 1
+ATOM 1 H5T RC5 1 30.660 50.980 21.970 1.00 0.00
+ATOM 2 O5' RC5 1 30.140 50.180 21.880 1.00 0.00
+ATOM 3 C5' RC5 1 29.720 49.750 23.160 1.00 0.00
+ATOM 4 1H5' RC5 1 30.580 49.500 23.780 1.00 0.00
+ATOM 5 2H5' RC5 1 29.130 48.840 23.040 1.00 0.00
+ATOM 6 C4' RC5 1 28.830 50.750 23.890 1.00 0.00
+ATOM 7 H4' RC5 1 28.280 51.300 23.120 1.00 0.00
+ATOM 8 O4' RC5 1 27.950 50.020 24.710 1.00 0.00
+ATOM 9 C1' RC5 1 27.660 50.790 25.850 1.00 0.00
+ATOM 10 H1' RC5 1 26.600 50.970 26.030 1.00 0.00
+ATOM 11 N1 RC5 1 28.070 50.070 27.060 1.00 0.00
+ATOM 12 C6 RC5 1 28.750 48.880 27.090 1.00 0.00
+ATOM 13 H6 RC5 1 29.040 48.440 26.150 1.00 0.00
+ATOM 14 C5 RC5 1 29.080 48.290 28.260 1.00 0.00
+ATOM 15 H5 RC5 1 29.650 47.380 28.320 1.00 0.00
+ATOM 16 C4 RC5 1 28.810 49.030 29.460 1.00 0.00
+ATOM 17 N4 RC5 1 29.130 48.470 30.630 1.00 0.00
+ATOM 18 H41 RC5 1 29.440 47.510 30.700 1.00 0.00
+ATOM 19 H42 RC5 1 28.740 49.010 31.390 1.00 0.00
+ATOM 20 N3 RC5 1 28.030 50.120 29.490 1.00 0.00
+ATOM 21 C2 RC5 1 27.690 50.620 28.270 1.00 0.00
+ATOM 22 O2 RC5 1 27.030 51.660 28.360 1.00 0.00
+ATOM 23 C3' RC5 1 29.540 51.770 24.780 1.00 0.00
+ATOM 24 H3' RC5 1 30.380 51.300 25.290 1.00 0.00
+ATOM 25 C2' RC5 1 28.430 52.110 25.770 1.00 0.00
+ATOM 26 1H2' RC5 1 28.920 52.400 26.700 1.00 0.00
+ATOM 27 O2' RC5 1 27.680 53.180 25.250 1.00 0.00
+ATOM 28 2HO' RC5 1 28.160 54.000 25.360 1.00 0.00
+ATOM 29 O3' RC5 1 30.100 52.900 24.150 1.00 0.00
+ATOM 30 P RG 2 31.070 53.870 24.980 1.00 0.00
+ATOM 31 O1P RG 2 32.030 54.470 24.020 1.00 0.00
+ATOM 32 O2P RG 2 31.500 53.110 26.180 1.00 0.00
+ATOM 33 O5' RG 2 29.990 55.020 25.310 1.00 0.00
+ATOM 34 C5' RG 2 29.480 55.920 24.350 1.00 0.00
+ATOM 35 1H5' RG 2 28.900 55.340 23.630 1.00 0.00
+ATOM 36 2H5' RG 2 30.310 56.470 23.910 1.00 0.00
+ATOM 37 C4' RG 2 28.590 56.900 25.100 1.00 0.00
+ATOM 38 H4' RG 2 27.940 57.460 24.430 1.00 0.00
+ATOM 39 O4' RG 2 27.770 56.310 26.090 1.00 0.00
+ATOM 40 C1' RG 2 27.780 57.050 27.290 1.00 0.00
+ATOM 41 H1' RG 2 26.730 57.160 27.590 1.00 0.00
+ATOM 42 N9 RG 2 28.410 56.360 28.420 1.00 0.00
+ATOM 43 C8 RG 2 28.890 55.080 28.430 1.00 0.00
+ATOM 44 H8 RG 2 28.980 54.440 27.560 1.00 0.00
+ATOM 45 N7 RG 2 29.300 54.610 29.570 1.00 0.00
+ATOM 46 C5 RG 2 28.970 55.650 30.440 1.00 0.00
+ATOM 47 C6 RG 2 28.870 55.680 31.860 1.00 0.00
+ATOM 48 O6 RG 2 29.130 54.830 32.710 1.00 0.00
+ATOM 49 N1 RG 2 28.500 56.910 32.380 1.00 0.00
+ATOM 50 H1 RG 2 28.840 57.070 33.320 1.00 0.00
+ATOM 51 C2 RG 2 28.140 57.990 31.590 1.00 0.00
+ATOM 52 N2 RG 2 27.710 59.090 32.230 1.00 0.00
+ATOM 53 H21 RG 2 27.460 58.940 33.200 1.00 0.00
+ATOM 54 H22 RG 2 27.440 59.850 31.620 1.00 0.00
+ATOM 55 N3 RG 2 28.090 57.910 30.260 1.00 0.00
+ATOM 56 C4 RG 2 28.470 56.720 29.750 1.00 0.00
+ATOM 57 C3' RG 2 29.500 57.860 25.870 1.00 0.00
+ATOM 58 H3' RG 2 30.250 57.200 26.320 1.00 0.00
+ATOM 59 C2' RG 2 28.470 58.350 26.880 1.00 0.00
+ATOM 60 1H2' RG 2 28.970 58.820 27.730 1.00 0.00
+ATOM 61 O2' RG 2 27.440 59.140 26.350 1.00 0.00
+ATOM 62 2HO' RG 2 27.260 58.760 25.490 1.00 0.00
+ATOM 63 O3' RG 2 30.050 58.800 24.970 1.00 0.00
+ATOM 64 P RC 3 31.480 59.500 25.200 1.00 0.00
+ATOM 65 O1P RC 3 31.500 60.560 24.170 1.00 0.00
+ATOM 66 O2P RC 3 32.640 58.580 25.180 1.00 0.00
+ATOM 67 O5' RC 3 31.330 60.220 26.630 1.00 0.00
+ATOM 68 C5' RC 3 30.990 61.590 26.680 1.00 0.00
+ATOM 69 1H5' RC 3 30.120 61.790 26.060 1.00 0.00
+ATOM 70 2H5' RC 3 31.880 62.120 26.330 1.00 0.00
+ATOM 71 C4' RC 3 30.890 62.170 28.090 1.00 0.00
+ATOM 72 H4' RC 3 30.590 63.200 27.930 1.00 0.00
+ATOM 73 O4' RC 3 29.960 61.470 28.890 1.00 0.00
+ATOM 74 C1' RC 3 30.470 61.450 30.210 1.00 0.00
+ATOM 75 H1' RC 3 29.690 61.880 30.840 1.00 0.00
+ATOM 76 N1 RC 3 30.990 60.150 30.660 1.00 0.00
+ATOM 77 C6 RC 3 31.390 59.150 29.830 1.00 0.00
+ATOM 78 H6 RC 3 31.400 59.240 28.750 1.00 0.00
+ATOM 79 C5 RC 3 31.760 57.960 30.360 1.00 0.00
+ATOM 80 H5 RC 3 32.120 57.140 29.770 1.00 0.00
+ATOM 81 C4 RC 3 31.880 57.900 31.790 1.00 0.00
+ATOM 82 N4 RC 3 32.390 56.820 32.390 1.00 0.00
+ATOM 83 H41 RC 3 32.750 56.050 31.840 1.00 0.00
+ATOM 84 H42 RC 3 32.360 56.800 33.400 1.00 0.00
+ATOM 85 N3 RC 3 31.500 58.910 32.590 1.00 0.00
+ATOM 86 C2 RC 3 31.030 60.060 32.040 1.00 0.00
+ATOM 87 O2 RC 3 30.760 61.000 32.780 1.00 0.00
+ATOM 88 C3' RC 3 32.210 62.270 28.850 1.00 0.00
+ATOM 89 H3' RC 3 32.800 61.350 28.800 1.00 0.00
+ATOM 90 C2' RC 3 31.640 62.430 30.250 1.00 0.00
+ATOM 91 1H2' RC 3 32.310 62.180 31.070 1.00 0.00
+ATOM 92 O2' RC 3 31.160 63.750 30.330 1.00 0.00
+ATOM 93 2HO' RC 3 31.670 64.410 29.850 1.00 0.00
+ATOM 94 O3' RC 3 32.940 63.400 28.400 1.00 0.00
+ATOM 95 P RU 4 34.470 63.650 28.820 1.00 0.00
+ATOM 96 O1P RU 4 34.870 64.950 28.220 1.00 0.00
+ATOM 97 O2P RU 4 35.300 62.450 28.600 1.00 0.00
+ATOM 98 O5' RU 4 34.390 63.920 30.410 1.00 0.00
+ATOM 99 C5' RU 4 34.230 65.210 30.960 1.00 0.00
+ATOM 100 1H5' RU 4 33.320 65.650 30.540 1.00 0.00
+ATOM 101 2H5' RU 4 35.060 65.830 30.610 1.00 0.00
+ATOM 102 C4' RU 4 34.150 65.220 32.480 1.00 0.00
+ATOM 103 H4' RU 4 33.690 66.150 32.810 1.00 0.00
+ATOM 104 O4' RU 4 33.300 64.240 33.040 1.00 0.00
+ATOM 105 C1' RU 4 33.820 63.740 34.250 1.00 0.00
+ATOM 106 H1' RU 4 33.100 63.760 35.060 1.00 0.00
+ATOM 107 N1 RU 4 34.320 62.370 34.020 1.00 0.00
+ATOM 108 C6 RU 4 34.440 61.780 32.800 1.00 0.00
+ATOM 109 H6 RU 4 34.240 62.360 31.910 1.00 0.00
+ATOM 110 C5 RU 4 34.850 60.500 32.660 1.00 0.00
+ATOM 111 H5 RU 4 35.070 60.120 31.680 1.00 0.00
+ATOM 112 C4 RU 4 35.190 59.660 33.790 1.00 0.00
+ATOM 113 O4 RU 4 35.740 58.560 33.730 1.00 0.00
+ATOM 114 N3 RU 4 34.980 60.300 35.000 1.00 0.00
+ATOM 115 H3 RU 4 35.230 59.750 35.800 1.00 0.00
+ATOM 116 C2 RU 4 34.610 61.630 35.160 1.00 0.00
+ATOM 117 O2 RU 4 34.500 62.050 36.310 1.00 0.00
+ATOM 118 C3' RU 4 35.500 65.110 33.190 1.00 0.00
+ATOM 119 H3' RU 4 36.170 64.410 32.690 1.00 0.00
+ATOM 120 C2' RU 4 35.010 64.640 34.560 1.00 0.00
+ATOM 121 1H2' RU 4 35.840 64.140 35.050 1.00 0.00
+ATOM 122 O2' RU 4 34.420 65.630 35.380 1.00 0.00
+ATOM 123 2HO' RU 4 34.240 66.370 34.800 1.00 0.00
+ATOM 124 O3' RU 4 36.170 66.350 33.160 1.00 0.00
+ATOM 125 P RU 5 37.760 66.400 33.430 1.00 0.00
+ATOM 126 O1P RU 5 38.260 67.790 33.410 1.00 0.00
+ATOM 127 O2P RU 5 38.310 65.420 32.470 1.00 0.00
+ATOM 128 O5' RU 5 37.960 65.810 34.910 1.00 0.00
+ATOM 129 C5' RU 5 37.770 66.570 36.090 1.00 0.00
+ATOM 130 1H5' RU 5 36.790 67.050 36.160 1.00 0.00
+ATOM 131 2H5' RU 5 38.480 67.400 36.010 1.00 0.00
+ATOM 132 C4' RU 5 38.020 65.740 37.340 1.00 0.00
+ATOM 133 H4' RU 5 37.590 66.270 38.190 1.00 0.00
+ATOM 134 O4' RU 5 37.280 64.540 37.230 1.00 0.00
+ATOM 135 C1' RU 5 38.000 63.440 37.730 1.00 0.00
+ATOM 136 H1' RU 5 37.480 63.010 38.590 1.00 0.00
+ATOM 137 N1 RU 5 38.150 62.330 36.780 1.00 0.00
+ATOM 138 C6 RU 5 37.910 62.320 35.430 1.00 0.00
+ATOM 139 H6 RU 5 37.640 63.240 34.930 1.00 0.00
+ATOM 140 C5 RU 5 38.100 61.270 34.610 1.00 0.00
+ATOM 141 H5 RU 5 38.030 61.300 33.530 1.00 0.00
+ATOM 142 C4 RU 5 38.550 59.990 35.100 1.00 0.00
+ATOM 143 O4 RU 5 38.730 58.910 34.530 1.00 0.00
+ATOM 144 N3 RU 5 38.670 60.000 36.480 1.00 0.00
+ATOM 145 H3 RU 5 38.830 59.120 36.960 1.00 0.00
+ATOM 146 C2 RU 5 38.460 61.090 37.310 1.00 0.00
+ATOM 147 O2 RU 5 38.490 60.810 38.510 1.00 0.00
+ATOM 148 C3' RU 5 39.450 65.280 37.590 1.00 0.00
+ATOM 149 H3' RU 5 39.850 65.080 36.590 1.00 0.00
+ATOM 150 C2' RU 5 39.300 63.970 38.350 1.00 0.00
+ATOM 151 1H2' RU 5 40.180 63.330 38.320 1.00 0.00
+ATOM 152 O2' RU 5 38.960 64.270 39.690 1.00 0.00
+ATOM 153 2HO' RU 5 39.100 65.210 39.800 1.00 0.00
+ATOM 154 O3' RU 5 40.300 66.100 38.360 1.00 0.00
+ATOM 155 P RC 6 41.890 66.080 38.070 1.00 0.00
+ATOM 156 O1P RC 6 42.550 67.200 38.770 1.00 0.00
+ATOM 157 O2P RC 6 42.040 65.890 36.610 1.00 0.00
+ATOM 158 O5' RC 6 42.330 64.700 38.790 1.00 0.00
+ATOM 159 C5' RC 6 42.340 64.670 40.200 1.00 0.00
+ATOM 160 1H5' RC 6 41.360 64.940 40.600 1.00 0.00
+ATOM 161 2H5' RC 6 43.050 65.410 40.560 1.00 0.00
+ATOM 162 C4' RC 6 42.760 63.280 40.680 1.00 0.00
+ATOM 163 H4' RC 6 42.730 63.420 41.760 1.00 0.00
+ATOM 164 O4' RC 6 41.820 62.250 40.460 1.00 0.00
+ATOM 165 C1' RC 6 42.510 61.030 40.380 1.00 0.00
+ATOM 166 H1' RC 6 42.040 60.410 41.140 1.00 0.00
+ATOM 167 N1 RC 6 42.450 60.400 39.050 1.00 0.00
+ATOM 168 C6 RC 6 42.030 61.080 37.940 1.00 0.00
+ATOM 169 H6 RC 6 41.970 62.160 37.910 1.00 0.00
+ATOM 170 C5 RC 6 41.960 60.470 36.740 1.00 0.00
+ATOM 171 H5 RC 6 41.700 60.940 35.800 1.00 0.00
+ATOM 172 C4 RC 6 42.250 59.070 36.670 1.00 0.00
+ATOM 173 N4 RC 6 42.110 58.380 35.530 1.00 0.00
+ATOM 174 H41 RC 6 41.760 58.790 34.680 1.00 0.00
+ATOM 175 H42 RC 6 42.410 57.420 35.620 1.00 0.00
+ATOM 176 N3 RC 6 42.680 58.430 37.760 1.00 0.00
+ATOM 177 C2 RC 6 42.800 59.060 38.960 1.00 0.00
+ATOM 178 O2 RC 6 43.240 58.400 39.900 1.00 0.00
+ATOM 179 C3' RC 6 44.150 62.750 40.330 1.00 0.00
+ATOM 180 H3' RC 6 44.230 62.800 39.240 1.00 0.00
+ATOM 181 C2' RC 6 43.940 61.320 40.820 1.00 0.00
+ATOM 182 1H2' RC 6 44.650 60.750 40.220 1.00 0.00
+ATOM 183 O2' RC 6 44.070 61.260 42.230 1.00 0.00
+ATOM 184 2HO' RC 6 44.510 60.430 42.400 1.00 0.00
+ATOM 185 O3' RC 6 45.260 63.390 40.910 1.00 0.00
+ATOM 186 P RA 7 46.600 63.620 40.050 1.00 0.00
+ATOM 187 O1P RA 7 47.600 64.310 40.900 1.00 0.00
+ATOM 188 O2P RA 7 46.140 64.190 38.760 1.00 0.00
+ATOM 189 O5' RA 7 47.160 62.150 39.720 1.00 0.00
+ATOM 190 C5' RA 7 47.730 61.430 40.790 1.00 0.00
+ATOM 191 1H5' RA 7 47.330 61.680 41.770 1.00 0.00
+ATOM 192 2H5' RA 7 48.740 61.820 40.920 1.00 0.00
+ATOM 193 C4' RA 7 47.910 59.940 40.510 1.00 0.00
+ATOM 194 H4' RA 7 48.390 59.480 41.380 1.00 0.00
+ATOM 195 O4' RA 7 46.750 59.240 40.140 1.00 0.00
+ATOM 196 C1' RA 7 47.000 58.050 39.420 1.00 0.00
+ATOM 197 H1' RA 7 46.600 57.200 39.970 1.00 0.00
+ATOM 198 N9 RA 7 46.450 58.130 38.050 1.00 0.00
+ATOM 199 C8 RA 7 46.040 59.150 37.230 1.00 0.00
+ATOM 200 H8 RA 7 45.910 60.150 37.610 1.00 0.00
+ATOM 201 N7 RA 7 45.600 58.730 36.080 1.00 0.00
+ATOM 202 C5 RA 7 45.850 57.360 36.080 1.00 0.00
+ATOM 203 C6 RA 7 45.830 56.330 35.120 1.00 0.00
+ATOM 204 N6 RA 7 45.680 56.380 33.790 1.00 0.00
+ATOM 205 H61 RA 7 45.730 57.240 33.270 1.00 0.00
+ATOM 206 H62 RA 7 45.770 55.460 33.390 1.00 0.00
+ATOM 207 N1 RA 7 46.180 55.070 35.430 1.00 0.00
+ATOM 208 C2 RA 7 46.670 54.820 36.630 1.00 0.00
+ATOM 209 H2 RA 7 47.070 53.840 36.840 1.00 0.00
+ATOM 210 N3 RA 7 46.880 55.760 37.540 1.00 0.00
+ATOM 211 C4 RA 7 46.380 56.990 37.290 1.00 0.00
+ATOM 212 C3' RA 7 48.930 59.450 39.490 1.00 0.00
+ATOM 213 H3' RA 7 48.770 60.010 38.570 1.00 0.00
+ATOM 214 C2' RA 7 48.510 58.000 39.280 1.00 0.00
+ATOM 215 1H2' RA 7 48.780 57.660 38.280 1.00 0.00
+ATOM 216 O2' RA 7 48.770 56.990 40.240 1.00 0.00
+ATOM 217 2HO' RA 7 49.430 56.350 39.950 1.00 0.00
+ATOM 218 O3' RA 7 50.230 59.730 39.970 1.00 0.00
+ATOM 219 P RU 8 51.450 59.420 38.970 1.00 0.00
+ATOM 220 O1P RU 8 52.600 59.750 39.840 1.00 0.00
+ATOM 221 O2P RU 8 51.260 60.060 37.650 1.00 0.00
+ATOM 222 O5' RU 8 51.370 57.810 38.870 1.00 0.00
+ATOM 223 C5' RU 8 51.940 56.960 39.840 1.00 0.00
+ATOM 224 1H5' RU 8 51.400 56.870 40.780 1.00 0.00
+ATOM 225 2H5' RU 8 52.920 57.310 40.160 1.00 0.00
+ATOM 226 C4' RU 8 52.080 55.510 39.380 1.00 0.00
+ATOM 227 H4' RU 8 52.350 54.910 40.250 1.00 0.00
+ATOM 228 O4' RU 8 50.850 55.020 38.910 1.00 0.00
+ATOM 229 C1' RU 8 51.030 54.030 37.920 1.00 0.00
+ATOM 230 H1' RU 8 50.660 53.090 38.310 1.00 0.00
+ATOM 231 N1 RU 8 50.360 54.500 36.690 1.00 0.00
+ATOM 232 C6 RU 8 50.060 55.800 36.420 1.00 0.00
+ATOM 233 H6 RU 8 50.230 56.560 37.170 1.00 0.00
+ATOM 234 C5 RU 8 49.540 56.190 35.240 1.00 0.00
+ATOM 235 H5 RU 8 49.270 57.200 34.980 1.00 0.00
+ATOM 236 C4 RU 8 49.310 55.260 34.160 1.00 0.00
+ATOM 237 O4 RU 8 48.840 55.480 33.040 1.00 0.00
+ATOM 238 N3 RU 8 49.690 53.980 34.520 1.00 0.00
+ATOM 239 H3 RU 8 49.690 53.270 33.810 1.00 0.00
+ATOM 240 C2 RU 8 50.230 53.520 35.710 1.00 0.00
+ATOM 241 O2 RU 8 50.620 52.360 35.830 1.00 0.00
+ATOM 242 C3' RU 8 53.090 55.360 38.240 1.00 0.00
+ATOM 243 H3' RU 8 53.000 56.150 37.500 1.00 0.00
+ATOM 244 C2' RU 8 52.540 54.040 37.700 1.00 0.00
+ATOM 245 1H2' RU 8 52.710 53.910 36.630 1.00 0.00
+ATOM 246 O2' RU 8 53.070 52.960 38.440 1.00 0.00
+ATOM 247 2HO' RU 8 53.050 52.230 37.820 1.00 0.00
+ATOM 248 O3' RU 8 54.360 55.210 38.840 1.00 0.00
+ATOM 249 P RA 9 55.710 55.760 38.140 1.00 0.00
+ATOM 250 O1P RA 9 56.690 55.770 39.240 1.00 0.00
+ATOM 251 O2P RA 9 55.380 56.990 37.390 1.00 0.00
+ATOM 252 O5' RA 9 55.990 54.590 37.070 1.00 0.00
+ATOM 253 C5' RA 9 56.550 53.330 37.370 1.00 0.00
+ATOM 254 1H5' RA 9 56.090 52.800 38.210 1.00 0.00
+ATOM 255 2H5' RA 9 57.580 53.480 37.710 1.00 0.00
+ATOM 256 C4' RA 9 56.750 52.390 36.190 1.00 0.00
+ATOM 257 H4' RA 9 57.290 51.510 36.560 1.00 0.00
+ATOM 258 O4' RA 9 55.540 51.900 35.640 1.00 0.00
+ATOM 259 C1' RA 9 55.700 51.940 34.240 1.00 0.00
+ATOM 260 H1' RA 9 55.450 51.040 33.680 1.00 0.00
+ATOM 261 N9 RA 9 54.640 52.810 33.720 1.00 0.00
+ATOM 262 C8 RA 9 54.030 53.910 34.280 1.00 0.00
+ATOM 263 H8 RA 9 54.240 54.170 35.300 1.00 0.00
+ATOM 264 N7 RA 9 53.090 54.430 33.540 1.00 0.00
+ATOM 265 C5 RA 9 53.240 53.730 32.350 1.00 0.00
+ATOM 266 C6 RA 9 52.650 53.740 31.070 1.00 0.00
+ATOM 267 N6 RA 9 51.890 54.740 30.610 1.00 0.00
+ATOM 268 H61 RA 9 51.750 55.620 31.090 1.00 0.00
+ATOM 269 H62 RA 9 51.160 54.520 29.940 1.00 0.00
+ATOM 270 N1 RA 9 52.790 52.730 30.200 1.00 0.00
+ATOM 271 C2 RA 9 53.660 51.770 30.460 1.00 0.00
+ATOM 272 H2 RA 9 53.810 51.000 29.720 1.00 0.00
+ATOM 273 N3 RA 9 54.400 51.720 31.560 1.00 0.00
+ATOM 274 C4 RA 9 54.060 52.650 32.480 1.00 0.00
+ATOM 275 C3' RA 9 57.540 53.070 35.080 1.00 0.00
+ATOM 276 H3' RA 9 57.300 54.130 35.060 1.00 0.00
+ATOM 277 C2' RA 9 57.040 52.500 33.760 1.00 0.00
+ATOM 278 1H2' RA 9 56.990 53.260 32.980 1.00 0.00
+ATOM 279 O2' RA 9 57.830 51.380 33.410 1.00 0.00
+ATOM 280 2HO' RA 9 58.510 51.350 34.080 1.00 0.00
+ATOM 281 O3' RA 9 58.930 52.870 35.220 1.00 0.00
+ATOM 282 P RU 10 60.030 54.050 35.210 1.00 0.00
+ATOM 283 O1P RU 10 61.240 53.310 35.640 1.00 0.00
+ATOM 284 O2P RU 10 59.490 55.130 36.060 1.00 0.00
+ATOM 285 O5' RU 10 60.000 54.470 33.660 1.00 0.00
+ATOM 286 C5' RU 10 60.770 55.530 33.150 1.00 0.00
+ATOM 287 1H5' RU 10 61.830 55.270 33.080 1.00 0.00
+ATOM 288 2H5' RU 10 60.690 56.320 33.900 1.00 0.00
+ATOM 289 C4' RU 10 60.350 56.000 31.760 1.00 0.00
+ATOM 290 H4' RU 10 60.920 56.920 31.620 1.00 0.00
+ATOM 291 O4' RU 10 60.760 55.030 30.830 1.00 0.00
+ATOM 292 C1' RU 10 59.600 54.550 30.180 1.00 0.00
+ATOM 293 H1' RU 10 59.490 55.030 29.210 1.00 0.00
+ATOM 294 N1 RU 10 59.830 53.120 29.930 1.00 0.00
+ATOM 295 C6 RU 10 60.180 52.290 30.960 1.00 0.00
+ATOM 296 H6 RU 10 60.380 52.740 31.920 1.00 0.00
+ATOM 297 C5 RU 10 60.330 50.950 30.830 1.00 0.00
+ATOM 298 H5 RU 10 60.610 50.310 31.660 1.00 0.00
+ATOM 299 C4 RU 10 60.150 50.300 29.560 1.00 0.00
+ATOM 300 O4 RU 10 60.210 49.090 29.370 1.00 0.00
+ATOM 301 N3 RU 10 59.910 51.170 28.500 1.00 0.00
+ATOM 302 H3 RU 10 59.780 50.740 27.600 1.00 0.00
+ATOM 303 C2 RU 10 59.760 52.540 28.680 1.00 0.00
+ATOM 304 O2 RU 10 59.370 53.200 27.720 1.00 0.00
+ATOM 305 C3' RU 10 58.850 56.220 31.540 1.00 0.00
+ATOM 306 H3' RU 10 58.310 56.480 32.450 1.00 0.00
+ATOM 307 C2' RU 10 58.410 54.830 31.100 1.00 0.00
+ATOM 308 1H2' RU 10 58.390 54.090 31.910 1.00 0.00
+ATOM 309 O2' RU 10 57.160 54.870 30.460 1.00 0.00
+ATOM 310 2HO' RU 10 56.930 55.780 30.270 1.00 0.00
+ATOM 311 O3' RU 10 58.470 57.100 30.510 1.00 0.00
+ATOM 312 P RA 11 58.700 58.690 30.420 1.00 0.00
+ATOM 313 O1P RA 11 58.450 59.300 31.750 1.00 0.00
+ATOM 314 O2P RA 11 57.950 59.190 29.250 1.00 0.00
+ATOM 315 O5' RA 11 60.290 58.910 30.330 1.00 0.00
+ATOM 316 C5' RA 11 61.050 58.460 29.230 1.00 0.00
+ATOM 317 1H5' RA 11 60.450 58.560 28.330 1.00 0.00
+ATOM 318 2H5' RA 11 61.250 57.400 29.410 1.00 0.00
+ATOM 319 C4' RA 11 62.400 59.150 29.030 1.00 0.00
+ATOM 320 H4' RA 11 62.250 60.220 29.150 1.00 0.00
+ATOM 321 O4' RA 11 63.290 58.650 30.000 1.00 0.00
+ATOM 322 C1' RA 11 64.370 57.960 29.420 1.00 0.00
+ATOM 323 H1' RA 11 65.330 58.350 29.780 1.00 0.00
+ATOM 324 N9 RA 11 64.180 56.570 29.850 1.00 0.00
+ATOM 325 C8 RA 11 64.620 55.980 31.010 1.00 0.00
+ATOM 326 H8 RA 11 65.120 56.600 31.750 1.00 0.00
+ATOM 327 N7 RA 11 64.440 54.690 31.030 1.00 0.00
+ATOM 328 C5 RA 11 63.740 54.390 29.860 1.00 0.00
+ATOM 329 C6 RA 11 63.340 53.190 29.250 1.00 0.00
+ATOM 330 N6 RA 11 63.650 51.970 29.720 1.00 0.00
+ATOM 331 H61 RA 11 64.270 51.940 30.520 1.00 0.00
+ATOM 332 H62 RA 11 63.310 51.130 29.270 1.00 0.00
+ATOM 333 N1 RA 11 62.740 53.250 28.050 1.00 0.00
+ATOM 334 C2 RA 11 62.560 54.450 27.520 1.00 0.00
+ATOM 335 H2 RA 11 62.080 54.460 26.550 1.00 0.00
+ATOM 336 N3 RA 11 62.970 55.630 27.950 1.00 0.00
+ATOM 337 C4 RA 11 63.520 55.560 29.190 1.00 0.00
+ATOM 338 C3' RA 11 62.990 58.820 27.660 1.00 0.00
+ATOM 339 H3' RA 11 62.430 57.940 27.350 1.00 0.00
+ATOM 340 C2' RA 11 64.390 58.280 27.930 1.00 0.00
+ATOM 341 1H2' RA 11 64.690 57.440 27.300 1.00 0.00
+ATOM 342 O2' RA 11 65.310 59.320 27.690 1.00 0.00
+ATOM 343 2HO' RA 11 64.830 59.980 27.190 1.00 0.00
+ATOM 344 O3' RA 11 62.980 59.750 26.600 1.00 0.00
+ATOM 345 P RA 12 61.780 59.660 25.530 1.00 0.00
+ATOM 346 O1P RA 12 61.960 60.910 24.770 1.00 0.00
+ATOM 347 O2P RA 12 60.460 59.430 26.160 1.00 0.00
+ATOM 348 O5' RA 12 62.010 58.460 24.480 1.00 0.00
+ATOM 349 C5' RA 12 61.970 57.090 24.810 1.00 0.00
+ATOM 350 1H5' RA 12 61.100 57.080 25.470 1.00 0.00
+ATOM 351 2H5' RA 12 62.890 56.790 25.310 1.00 0.00
+ATOM 352 C4' RA 12 61.510 56.180 23.670 1.00 0.00
+ATOM 353 H4' RA 12 61.810 55.190 24.010 1.00 0.00
+ATOM 354 O4' RA 12 60.130 56.270 23.390 1.00 0.00
+ATOM 355 C1' RA 12 59.950 56.170 22.000 1.00 0.00
+ATOM 356 H1' RA 12 59.160 55.450 21.760 1.00 0.00
+ATOM 357 N9 RA 12 59.600 57.520 21.510 1.00 0.00
+ATOM 358 C8 RA 12 59.480 58.680 22.240 1.00 0.00
+ATOM 359 H8 RA 12 59.910 58.730 23.230 1.00 0.00
+ATOM 360 N7 RA 12 58.890 59.650 21.600 1.00 0.00
+ATOM 361 C5 RA 12 58.500 59.050 20.410 1.00 0.00
+ATOM 362 C6 RA 12 57.660 59.450 19.360 1.00 0.00
+ATOM 363 N6 RA 12 56.960 60.600 19.310 1.00 0.00
+ATOM 364 H61 RA 12 56.980 61.230 20.100 1.00 0.00
+ATOM 365 H62 RA 12 56.370 60.850 18.530 1.00 0.00
+ATOM 366 N1 RA 12 57.520 58.630 18.310 1.00 0.00
+ATOM 367 C2 RA 12 58.090 57.440 18.280 1.00 0.00
+ATOM 368 H2 RA 12 58.140 56.860 17.360 1.00 0.00
+ATOM 369 N3 RA 12 58.810 56.930 19.260 1.00 0.00
+ATOM 370 C4 RA 12 58.980 57.770 20.310 1.00 0.00
+ATOM 371 C3' RA 12 62.260 56.320 22.350 1.00 0.00
+ATOM 372 H3' RA 12 62.460 57.380 22.230 1.00 0.00
+ATOM 373 C2' RA 12 61.270 55.800 21.320 1.00 0.00
+ATOM 374 1H2' RA 12 61.380 56.390 20.410 1.00 0.00
+ATOM 375 O2' RA 12 61.220 54.430 21.000 1.00 0.00
+ATOM 376 2HO' RA 12 62.130 54.130 21.100 1.00 0.00
+ATOM 377 O3' RA 12 63.420 55.510 22.310 1.00 0.00
+ATOM 378 P RU 13 64.550 55.950 21.250 1.00 0.00
+ATOM 379 O1P RU 13 64.220 57.220 20.550 1.00 0.00
+ATOM 380 O2P RU 13 64.890 54.740 20.480 1.00 0.00
+ATOM 381 O5' RU 13 65.820 56.240 22.200 1.00 0.00
+ATOM 382 C5' RU 13 65.820 57.300 23.120 1.00 0.00
+ATOM 383 1H5' RU 13 64.830 57.740 23.050 1.00 0.00
+ATOM 384 2H5' RU 13 66.550 58.070 22.850 1.00 0.00
+ATOM 385 C4' RU 13 66.210 57.000 24.570 1.00 0.00
+ATOM 386 H4' RU 13 66.170 57.910 25.160 1.00 0.00
+ATOM 387 O4' RU 13 65.260 56.230 25.270 1.00 0.00
+ATOM 388 C1' RU 13 65.880 55.280 26.120 1.00 0.00
+ATOM 389 H1' RU 13 65.500 55.310 27.140 1.00 0.00
+ATOM 390 N1 RU 13 65.810 53.860 25.720 1.00 0.00
+ATOM 391 C6 RU 13 65.320 53.450 24.520 1.00 0.00
+ATOM 392 H6 RU 13 64.970 54.280 23.910 1.00 0.00
+ATOM 393 C5 RU 13 65.210 52.190 24.070 1.00 0.00
+ATOM 394 H5 RU 13 64.730 51.940 23.130 1.00 0.00
+ATOM 395 C4 RU 13 65.640 51.090 24.910 1.00 0.00
+ATOM 396 O4 RU 13 65.750 49.900 24.630 1.00 0.00
+ATOM 397 N3 RU 13 66.030 51.530 26.160 1.00 0.00
+ATOM 398 H3 RU 13 66.330 50.800 26.780 1.00 0.00
+ATOM 399 C2 RU 13 66.170 52.850 26.590 1.00 0.00
+ATOM 400 O2 RU 13 66.510 53.060 27.750 1.00 0.00
+ATOM 401 C3' RU 13 67.600 56.400 24.770 1.00 0.00
+ATOM 402 H3' RU 13 67.830 55.640 24.020 1.00 0.00
+ATOM 403 C2' RU 13 67.330 55.740 26.110 1.00 0.00
+ATOM 404 1H2' RU 13 68.020 54.900 26.230 1.00 0.00
+ATOM 405 O2' RU 13 67.460 56.590 27.230 1.00 0.00
+ATOM 406 2HO' RU 13 67.780 57.410 26.850 1.00 0.00
+ATOM 407 O3' RU 13 68.700 57.270 24.890 1.00 0.00
+ATOM 408 P RC 14 70.180 56.810 24.450 1.00 0.00
+ATOM 409 O1P RC 14 71.130 57.940 24.370 1.00 0.00
+ATOM 410 O2P RC 14 70.040 55.880 23.310 1.00 0.00
+ATOM 411 O5' RC 14 70.780 55.880 25.610 1.00 0.00
+ATOM 412 C5' RC 14 70.970 56.350 26.930 1.00 0.00
+ATOM 413 1H5' RC 14 70.050 56.880 27.200 1.00 0.00
+ATOM 414 2H5' RC 14 71.810 57.040 26.990 1.00 0.00
+ATOM 415 C4' RC 14 71.180 55.210 27.910 1.00 0.00
+ATOM 416 H4' RC 14 71.320 55.630 28.910 1.00 0.00
+ATOM 417 O4' RC 14 70.070 54.340 27.890 1.00 0.00
+ATOM 418 C1' RC 14 70.480 53.010 28.100 1.00 0.00
+ATOM 419 H1' RC 14 69.940 52.640 28.970 1.00 0.00
+ATOM 420 N1 RC 14 70.230 52.150 26.920 1.00 0.00
+ATOM 421 C6 RC 14 69.660 52.650 25.790 1.00 0.00
+ATOM 422 H6 RC 14 69.480 53.710 25.700 1.00 0.00
+ATOM 423 C5 RC 14 69.290 51.800 24.800 1.00 0.00
+ATOM 424 H5 RC 14 68.910 52.110 23.840 1.00 0.00
+ATOM 425 C4 RC 14 69.400 50.400 25.090 1.00 0.00
+ATOM 426 N4 RC 14 69.110 49.570 24.080 1.00 0.00
+ATOM 427 H41 RC 14 68.670 49.740 23.190 1.00 0.00
+ATOM 428 H42 RC 14 69.130 48.610 24.390 1.00 0.00
+ATOM 429 N3 RC 14 69.900 49.920 26.240 1.00 0.00
+ATOM 430 C2 RC 14 70.280 50.800 27.200 1.00 0.00
+ATOM 431 O2 RC 14 70.590 50.370 28.310 1.00 0.00
+ATOM 432 C3' RC 14 72.350 54.250 27.680 1.00 0.00
+ATOM 433 H3' RC 14 72.340 54.050 26.610 1.00 0.00
+ATOM 434 C2' RC 14 71.960 53.000 28.470 1.00 0.00
+ATOM 435 1H2' RC 14 72.520 52.140 28.090 1.00 0.00
+ATOM 436 O2' RC 14 72.120 53.120 29.860 1.00 0.00
+ATOM 437 2HO' RC 14 72.110 52.230 30.230 1.00 0.00
+ATOM 438 O3' RC 14 73.530 54.900 28.090 1.00 0.00
+ATOM 439 P RC 15 74.890 54.570 27.290 1.00 0.00
+ATOM 440 O1P RC 15 76.020 55.280 27.930 1.00 0.00
+ATOM 441 O2P RC 15 74.650 54.720 25.830 1.00 0.00
+ATOM 442 O5' RC 15 75.070 52.990 27.520 1.00 0.00
+ATOM 443 C5' RC 15 75.480 52.590 28.800 1.00 0.00
+ATOM 444 1H5' RC 15 74.880 52.950 29.640 1.00 0.00
+ATOM 445 2H5' RC 15 76.490 52.990 28.860 1.00 0.00
+ATOM 446 C4' RC 15 75.580 51.060 28.800 1.00 0.00
+ATOM 447 H4' RC 15 76.010 50.760 29.760 1.00 0.00
+ATOM 448 O4' RC 15 74.350 50.390 28.620 1.00 0.00
+ATOM 449 C1' RC 15 74.700 49.180 27.990 1.00 0.00
+ATOM 450 H1' RC 15 74.230 48.390 28.580 1.00 0.00
+ATOM 451 N1 RC 15 74.170 49.090 26.620 1.00 0.00
+ATOM 452 C6 RC 15 73.720 50.160 25.910 1.00 0.00
+ATOM 453 H6 RC 15 73.870 51.150 26.320 1.00 0.00
+ATOM 454 C5 RC 15 72.970 50.040 24.790 1.00 0.00
+ATOM 455 H5 RC 15 72.570 50.910 24.300 1.00 0.00
+ATOM 456 C4 RC 15 72.790 48.680 24.360 1.00 0.00
+ATOM 457 N4 RC 15 71.970 48.480 23.310 1.00 0.00
+ATOM 458 H41 RC 15 71.770 49.250 22.700 1.00 0.00
+ATOM 459 H42 RC 15 71.860 47.540 22.970 1.00 0.00
+ATOM 460 N3 RC 15 73.340 47.600 24.920 1.00 0.00
+ATOM 461 C2 RC 15 74.050 47.830 26.050 1.00 0.00
+ATOM 462 O2 RC 15 74.430 46.820 26.630 1.00 0.00
+ATOM 463 C3' RC 15 76.640 50.540 27.840 1.00 0.00
+ATOM 464 H3' RC 15 76.430 50.840 26.810 1.00 0.00
+ATOM 465 C2' RC 15 76.220 49.070 27.910 1.00 0.00
+ATOM 466 1H2' RC 15 76.560 48.610 26.980 1.00 0.00
+ATOM 467 O2' RC 15 76.630 48.360 29.050 1.00 0.00
+ATOM 468 2HO' RC 15 77.380 48.810 29.450 1.00 0.00
+ATOM 469 O3' RC 15 78.020 50.670 28.080 1.00 0.00
+ATOM 470 P RU 16 79.100 50.580 26.880 1.00 0.00
+ATOM 471 O1P RU 16 80.420 50.680 27.530 1.00 0.00
+ATOM 472 O2P RU 16 78.640 51.580 25.900 1.00 0.00
+ATOM 473 O5' RU 16 78.990 49.130 26.200 1.00 0.00
+ATOM 474 C5' RU 16 79.440 47.980 26.880 1.00 0.00
+ATOM 475 1H5' RU 16 78.920 48.050 27.840 1.00 0.00
+ATOM 476 2H5' RU 16 80.520 48.090 26.950 1.00 0.00
+ATOM 477 C4' RU 16 79.000 46.660 26.260 1.00 0.00
+ATOM 478 H4' RU 16 79.290 45.870 26.950 1.00 0.00
+ATOM 479 O4' RU 16 77.640 46.550 25.930 1.00 0.00
+ATOM 480 C1' RU 16 77.470 45.800 24.750 1.00 0.00
+ATOM 481 H1' RU 16 76.850 44.930 24.950 1.00 0.00
+ATOM 482 N1 RU 16 76.730 46.560 23.720 1.00 0.00
+ATOM 483 C6 RU 16 76.800 47.920 23.730 1.00 0.00
+ATOM 484 H6 RU 16 77.350 48.450 24.490 1.00 0.00
+ATOM 485 C5 RU 16 76.070 48.580 22.810 1.00 0.00
+ATOM 486 H5 RU 16 76.110 49.660 22.850 1.00 0.00
+ATOM 487 C4 RU 16 75.380 47.890 21.740 1.00 0.00
+ATOM 488 O4 RU 16 74.770 48.410 20.810 1.00 0.00
+ATOM 489 N3 RU 16 75.370 46.500 21.780 1.00 0.00
+ATOM 490 H3 RU 16 74.720 46.100 21.120 1.00 0.00
+ATOM 491 C2 RU 16 76.010 45.810 22.810 1.00 0.00
+ATOM 492 O2 RU 16 75.850 44.600 22.860 1.00 0.00
+ATOM 493 C3' RU 16 79.740 46.450 24.940 1.00 0.00
+ATOM 494 H3' RU 16 79.800 47.340 24.310 1.00 0.00
+ATOM 495 C2' RU 16 78.850 45.440 24.220 1.00 0.00
+ATOM 496 1H2' RU 16 78.980 45.480 23.140 1.00 0.00
+ATOM 497 O2' RU 16 79.120 44.110 24.600 1.00 0.00
+ATOM 498 2HO' RU 16 80.060 43.910 24.560 1.00 0.00
+ATOM 499 O3' RU 16 81.070 46.050 25.190 1.00 0.00
+ATOM 500 P RA 17 82.130 45.890 23.990 1.00 0.00
+ATOM 501 O1P RA 17 83.500 45.670 24.510 1.00 0.00
+ATOM 502 O2P RA 17 81.860 46.870 22.920 1.00 0.00
+ATOM 503 O5' RA 17 81.620 44.470 23.430 1.00 0.00
+ATOM 504 C5' RA 17 82.090 43.190 23.790 1.00 0.00
+ATOM 505 1H5' RA 17 81.670 42.830 24.730 1.00 0.00
+ATOM 506 2H5' RA 17 83.170 43.240 23.930 1.00 0.00
+ATOM 507 C4' RA 17 81.700 42.190 22.710 1.00 0.00
+ATOM 508 H4' RA 17 82.200 41.270 23.020 1.00 0.00
+ATOM 509 O4' RA 17 80.300 42.110 22.570 1.00 0.00
+ATOM 510 C1' RA 17 80.000 41.930 21.200 1.00 0.00
+ATOM 511 H1' RA 17 79.400 41.030 21.110 1.00 0.00
+ATOM 512 N9 RA 17 79.290 43.120 20.700 1.00 0.00
+ATOM 513 C8 RA 17 79.480 44.440 21.030 1.00 0.00
+ATOM 514 H8 RA 17 80.300 44.780 21.640 1.00 0.00
+ATOM 515 N7 RA 17 78.760 45.260 20.320 1.00 0.00
+ATOM 516 C5 RA 17 77.970 44.410 19.550 1.00 0.00
+ATOM 517 C6 RA 17 77.020 44.700 18.560 1.00 0.00
+ATOM 518 N6 RA 17 76.620 45.960 18.320 1.00 0.00
+ATOM 519 H61 RA 17 77.100 46.700 18.820 1.00 0.00
+ATOM 520 H62 RA 17 75.940 46.150 17.600 1.00 0.00
+ATOM 521 N1 RA 17 76.540 43.670 17.840 1.00 0.00
+ATOM 522 C2 RA 17 76.900 42.430 18.160 1.00 0.00
+ATOM 523 H2 RA 17 76.480 41.640 17.550 1.00 0.00
+ATOM 524 N3 RA 17 77.780 42.050 19.060 1.00 0.00
+ATOM 525 C4 RA 17 78.330 43.100 19.710 1.00 0.00
+ATOM 526 C3' RA 17 82.280 42.480 21.330 1.00 0.00
+ATOM 527 H3' RA 17 82.080 43.530 21.100 1.00 0.00
+ATOM 528 C2' RA 17 81.320 41.630 20.490 1.00 0.00
+ATOM 529 1H2' RA 17 81.310 42.050 19.490 1.00 0.00
+ATOM 530 O2' RA 17 81.590 40.250 20.510 1.00 0.00
+ATOM 531 2HO' RA 17 82.510 40.090 20.720 1.00 0.00
+ATOM 532 O3' RA 17 83.650 42.270 21.120 1.00 0.00
+ATOM 533 P RA 18 84.400 42.940 19.860 1.00 0.00
+ATOM 534 O1P RA 18 85.830 42.580 19.990 1.00 0.00
+ATOM 535 O2P RA 18 84.070 44.380 19.880 1.00 0.00
+ATOM 536 O5' RA 18 83.860 42.290 18.480 1.00 0.00
+ATOM 537 C5' RA 18 84.150 40.950 18.140 1.00 0.00
+ATOM 538 1H5' RA 18 83.860 40.370 19.020 1.00 0.00
+ATOM 539 2H5' RA 18 85.180 40.940 17.780 1.00 0.00
+ATOM 540 C4' RA 18 83.240 40.500 17.000 1.00 0.00
+ATOM 541 H4' RA 18 83.380 39.420 16.920 1.00 0.00
+ATOM 542 O4' RA 18 81.900 40.690 17.390 1.00 0.00
+ATOM 543 C1' RA 18 81.140 41.200 16.310 1.00 0.00
+ATOM 544 H1' RA 18 80.280 40.560 16.130 1.00 0.00
+ATOM 545 N9 RA 18 80.670 42.580 16.470 1.00 0.00
+ATOM 546 C8 RA 18 81.130 43.640 17.210 1.00 0.00
+ATOM 547 H8 RA 18 81.900 43.490 17.950 1.00 0.00
+ATOM 548 N7 RA 18 80.470 44.760 17.060 1.00 0.00
+ATOM 549 C5 RA 18 79.560 44.460 16.050 1.00 0.00
+ATOM 550 C6 RA 18 78.630 45.220 15.320 1.00 0.00
+ATOM 551 N6 RA 18 78.580 46.560 15.370 1.00 0.00
+ATOM 552 H61 RA 18 79.020 46.920 16.210 1.00 0.00
+ATOM 553 H62 RA 18 77.740 46.960 14.980 1.00 0.00
+ATOM 554 N1 RA 18 77.920 44.650 14.340 1.00 0.00
+ATOM 555 C2 RA 18 78.080 43.350 14.160 1.00 0.00
+ATOM 556 H2 RA 18 77.410 42.940 13.410 1.00 0.00
+ATOM 557 N3 RA 18 78.900 42.520 14.780 1.00 0.00
+ATOM 558 C4 RA 18 79.660 43.140 15.730 1.00 0.00
+ATOM 559 C3' RA 18 83.480 41.270 15.710 1.00 0.00
+ATOM 560 H3' RA 18 83.590 42.340 15.890 1.00 0.00
+ATOM 561 C2' RA 18 82.090 41.070 15.120 1.00 0.00
+ATOM 562 1H2' RA 18 81.850 41.780 14.320 1.00 0.00
+ATOM 563 O2' RA 18 81.910 39.740 14.690 1.00 0.00
+ATOM 564 2HO' RA 18 82.760 39.550 14.300 1.00 0.00
+ATOM 565 O3' RA 18 84.500 40.830 14.850 1.00 0.00
+ATOM 566 P RU 19 85.260 41.870 13.890 1.00 0.00
+ATOM 567 O1P RU 19 85.960 40.990 12.930 1.00 0.00
+ATOM 568 O2P RU 19 86.040 42.880 14.650 1.00 0.00
+ATOM 569 O5' RU 19 84.010 42.500 13.100 1.00 0.00
+ATOM 570 C5' RU 19 83.280 41.790 12.140 1.00 0.00
+ATOM 571 1H5' RU 19 82.820 40.890 12.560 1.00 0.00
+ATOM 572 2H5' RU 19 83.880 41.540 11.270 1.00 0.00
+ATOM 573 C4' RU 19 82.190 42.650 11.510 1.00 0.00
+ATOM 574 H4' RU 19 81.680 42.000 10.800 1.00 0.00
+ATOM 575 O4' RU 19 81.250 43.290 12.360 1.00 0.00
+ATOM 576 C1' RU 19 80.910 44.540 11.810 1.00 0.00
+ATOM 577 H1' RU 19 79.850 44.660 11.600 1.00 0.00
+ATOM 578 N1 RU 19 81.290 45.680 12.670 1.00 0.00
+ATOM 579 C6 RU 19 82.170 45.550 13.710 1.00 0.00
+ATOM 580 H6 RU 19 82.580 44.560 13.810 1.00 0.00
+ATOM 581 C5 RU 19 82.410 46.490 14.650 1.00 0.00
+ATOM 582 H5 RU 19 83.110 46.330 15.450 1.00 0.00
+ATOM 583 C4 RU 19 81.820 47.800 14.470 1.00 0.00
+ATOM 584 O4 RU 19 82.100 48.710 15.250 1.00 0.00
+ATOM 585 N3 RU 19 80.970 47.940 13.390 1.00 0.00
+ATOM 586 H3 RU 19 80.470 48.810 13.270 1.00 0.00
+ATOM 587 C2 RU 19 80.610 46.880 12.570 1.00 0.00
+ATOM 588 O2 RU 19 79.760 47.070 11.700 1.00 0.00
+ATOM 589 C3' RU 19 82.760 43.820 10.710 1.00 0.00
+ATOM 590 H3' RU 19 83.490 44.370 11.290 1.00 0.00
+ATOM 591 C2' RU 19 81.580 44.750 10.460 1.00 0.00
+ATOM 592 1H2' RU 19 81.860 45.790 10.260 1.00 0.00
+ATOM 593 O2' RU 19 80.770 44.330 9.390 1.00 0.00
+ATOM 594 2HO' RU 19 81.370 44.000 8.710 1.00 0.00
+ATOM 595 O3' RU 19 83.360 43.400 9.500 1.00 0.00
+ATOM 596 P RG 20 84.480 44.290 8.770 1.00 0.00
+ATOM 597 O1P RG 20 84.940 43.640 7.520 1.00 0.00
+ATOM 598 O2P RG 20 85.540 44.560 9.770 1.00 0.00
+ATOM 599 O5' RG 20 83.930 45.750 8.380 1.00 0.00
+ATOM 600 C5' RG 20 82.970 45.890 7.350 1.00 0.00
+ATOM 601 1H5' RG 20 82.200 45.120 7.380 1.00 0.00
+ATOM 602 2H5' RG 20 83.500 45.720 6.410 1.00 0.00
+ATOM 603 C4' RG 20 82.380 47.290 7.340 1.00 0.00
+ATOM 604 H4' RG 20 81.650 47.250 6.530 1.00 0.00
+ATOM 605 O4' RG 20 81.850 47.680 8.590 1.00 0.00
+ATOM 606 C1' RG 20 81.500 49.040 8.510 1.00 0.00
+ATOM 607 H1' RG 20 80.460 49.140 8.190 1.00 0.00
+ATOM 608 N9 RG 20 81.580 49.680 9.840 1.00 0.00
+ATOM 609 C8 RG 20 82.290 49.350 10.970 1.00 0.00
+ATOM 610 H8 RG 20 82.710 48.370 11.130 1.00 0.00
+ATOM 611 N7 RG 20 82.500 50.340 11.790 1.00 0.00
+ATOM 612 C5 RG 20 81.790 51.370 11.190 1.00 0.00
+ATOM 613 C6 RG 20 81.540 52.720 11.570 1.00 0.00
+ATOM 614 O6 RG 20 81.950 53.370 12.530 1.00 0.00
+ATOM 615 N1 RG 20 80.750 53.490 10.730 1.00 0.00
+ATOM 616 H1 RG 20 80.330 54.340 11.070 1.00 0.00
+ATOM 617 C2 RG 20 80.400 53.020 9.480 1.00 0.00
+ATOM 618 N2 RG 20 79.680 53.850 8.710 1.00 0.00
+ATOM 619 H21 RG 20 79.570 54.770 9.120 1.00 0.00
+ATOM 620 H22 RG 20 79.370 53.530 7.810 1.00 0.00
+ATOM 621 N3 RG 20 80.560 51.750 9.090 1.00 0.00
+ATOM 622 C4 RG 20 81.290 51.020 9.970 1.00 0.00
+ATOM 623 C3' RG 20 83.270 48.480 7.010 1.00 0.00
+ATOM 624 H3' RG 20 84.210 48.410 7.550 1.00 0.00
+ATOM 625 C2' RG 20 82.450 49.670 7.500 1.00 0.00
+ATOM 626 1H2' RG 20 83.060 50.490 7.890 1.00 0.00
+ATOM 627 O2' RG 20 81.700 50.300 6.480 1.00 0.00
+ATOM 628 2HO' RG 20 82.380 50.740 5.960 1.00 0.00
+ATOM 629 O3' RG 20 83.530 48.520 5.620 1.00 0.00
+ATOM 630 P RA 21 84.730 49.450 5.090 1.00 0.00
+ATOM 631 O1P RA 21 85.230 48.780 3.860 1.00 0.00
+ATOM 632 O2P RA 21 85.790 49.610 6.110 1.00 0.00
+ATOM 633 O5' RA 21 84.020 50.870 4.860 1.00 0.00
+ATOM 634 C5' RA 21 83.180 51.100 3.750 1.00 0.00
+ATOM 635 1H5' RA 21 82.480 50.260 3.730 1.00 0.00
+ATOM 636 2H5' RA 21 83.830 51.060 2.880 1.00 0.00
+ATOM 637 C4' RA 21 82.500 52.450 3.910 1.00 0.00
+ATOM 638 H4' RA 21 81.750 52.530 3.120 1.00 0.00
+ATOM 639 O4' RA 21 81.890 52.720 5.160 1.00 0.00
+ATOM 640 C1' RA 21 81.820 54.110 5.380 1.00 0.00
+ATOM 641 H1' RA 21 80.790 54.480 5.320 1.00 0.00
+ATOM 642 N9 RA 21 82.470 54.490 6.640 1.00 0.00
+ATOM 643 C8 RA 21 82.970 53.600 7.560 1.00 0.00
+ATOM 644 H8 RA 21 83.010 52.520 7.490 1.00 0.00
+ATOM 645 N7 RA 21 83.340 54.230 8.640 1.00 0.00
+ATOM 646 C5 RA 21 82.840 55.520 8.520 1.00 0.00
+ATOM 647 C6 RA 21 82.800 56.690 9.300 1.00 0.00
+ATOM 648 N6 RA 21 83.430 56.740 10.480 1.00 0.00
+ATOM 649 H61 RA 21 84.030 55.950 10.690 1.00 0.00
+ATOM 650 H62 RA 21 83.570 57.620 10.950 1.00 0.00
+ATOM 651 N1 RA 21 82.360 57.870 8.850 1.00 0.00
+ATOM 652 C2 RA 21 81.870 57.880 7.620 1.00 0.00
+ATOM 653 H2 RA 21 81.470 58.840 7.330 1.00 0.00
+ATOM 654 N3 RA 21 81.890 56.880 6.760 1.00 0.00
+ATOM 655 C4 RA 21 82.290 55.690 7.280 1.00 0.00
+ATOM 656 C3' RA 21 83.520 53.580 3.770 1.00 0.00
+ATOM 657 H3' RA 21 84.220 53.410 4.580 1.00 0.00
+ATOM 658 C2' RA 21 82.650 54.730 4.260 1.00 0.00
+ATOM 659 1H2' RA 21 83.240 55.530 4.700 1.00 0.00
+ATOM 660 O2' RA 21 81.740 55.200 3.280 1.00 0.00
+ATOM 661 2HO' RA 21 81.450 56.090 3.500 1.00 0.00
+ATOM 662 O3' RA 21 84.060 53.630 2.470 1.00 0.00
+ATOM 663 P RU 22 85.450 54.440 2.390 1.00 0.00
+ATOM 664 O1P RU 22 85.920 54.210 1.010 1.00 0.00
+ATOM 665 O2P RU 22 86.330 53.940 3.470 1.00 0.00
+ATOM 666 O5' RU 22 85.260 56.020 2.640 1.00 0.00
+ATOM 667 C5' RU 22 84.240 56.760 2.000 1.00 0.00
+ATOM 668 1H5' RU 22 83.350 56.130 1.940 1.00 0.00
+ATOM 669 2H5' RU 22 84.510 57.000 0.970 1.00 0.00
+ATOM 670 C4' RU 22 83.860 58.060 2.690 1.00 0.00
+ATOM 671 H4' RU 22 82.990 58.480 2.190 1.00 0.00
+ATOM 672 O4' RU 22 83.630 57.890 4.070 1.00 0.00
+ATOM 673 C1' RU 22 84.520 58.720 4.780 1.00 0.00
+ATOM 674 H1' RU 22 84.150 59.740 4.920 1.00 0.00
+ATOM 675 N1 RU 22 84.960 58.190 6.080 1.00 0.00
+ATOM 676 C6 RU 22 85.370 56.890 6.200 1.00 0.00
+ATOM 677 H6 RU 22 85.320 56.220 5.360 1.00 0.00
+ATOM 678 C5 RU 22 85.870 56.470 7.380 1.00 0.00
+ATOM 679 H5 RU 22 86.240 55.460 7.450 1.00 0.00
+ATOM 680 C4 RU 22 86.000 57.340 8.530 1.00 0.00
+ATOM 681 O4 RU 22 86.460 57.010 9.620 1.00 0.00
+ATOM 682 N3 RU 22 85.510 58.620 8.310 1.00 0.00
+ATOM 683 H3 RU 22 85.520 59.230 9.110 1.00 0.00
+ATOM 684 C2 RU 22 85.040 59.120 7.100 1.00 0.00
+ATOM 685 O2 RU 22 84.660 60.290 7.120 1.00 0.00
+ATOM 686 C3' RU 22 85.130 58.900 2.520 1.00 0.00
+ATOM 687 H3' RU 22 85.840 58.560 1.770 1.00 0.00
+ATOM 688 C2' RU 22 85.760 58.760 3.900 1.00 0.00
+ATOM 689 1H2' RU 22 86.330 57.830 4.000 1.00 0.00
+ATOM 690 O2' RU 22 86.550 59.900 4.190 1.00 0.00
+ATOM 691 2HO' RU 22 86.750 60.410 3.400 1.00 0.00
+ATOM 692 O3' RU 22 84.710 60.210 2.230 1.00 0.00
+ATOM 693 P RA 23 85.510 61.210 1.250 1.00 0.00
+ATOM 694 O1P RA 23 85.390 60.700 -0.130 1.00 0.00
+ATOM 695 O2P RA 23 86.840 61.350 1.870 1.00 0.00
+ATOM 696 O5' RA 23 84.610 62.540 1.400 1.00 0.00
+ATOM 697 C5' RA 23 83.390 62.660 0.710 1.00 0.00
+ATOM 698 1H5' RA 23 82.870 61.710 0.610 1.00 0.00
+ATOM 699 2H5' RA 23 83.650 62.970 -0.300 1.00 0.00
+ATOM 700 C4' RA 23 82.360 63.700 1.150 1.00 0.00
+ATOM 701 H4' RA 23 81.420 63.670 0.600 1.00 0.00
+ATOM 702 O4' RA 23 82.160 63.410 2.520 1.00 0.00
+ATOM 703 C1' RA 23 82.410 64.610 3.220 1.00 0.00
+ATOM 704 H1' RA 23 81.530 64.810 3.820 1.00 0.00
+ATOM 705 N9 RA 23 83.460 64.490 4.250 1.00 0.00
+ATOM 706 C8 RA 23 84.260 63.410 4.520 1.00 0.00
+ATOM 707 H8 RA 23 84.310 62.470 3.990 1.00 0.00
+ATOM 708 N7 RA 23 85.060 63.670 5.520 1.00 0.00
+ATOM 709 C5 RA 23 84.730 64.930 5.990 1.00 0.00
+ATOM 710 C6 RA 23 85.240 65.890 6.880 1.00 0.00
+ATOM 711 N6 RA 23 86.410 65.850 7.530 1.00 0.00
+ATOM 712 H61 RA 23 86.850 64.940 7.500 1.00 0.00
+ATOM 713 H62 RA 23 86.730 66.740 7.890 1.00 0.00
+ATOM 714 N1 RA 23 84.730 67.120 6.990 1.00 0.00
+ATOM 715 C2 RA 23 83.790 67.420 6.100 1.00 0.00
+ATOM 716 H2 RA 23 83.450 68.440 6.120 1.00 0.00
+ATOM 717 N3 RA 23 83.250 66.710 5.120 1.00 0.00
+ATOM 718 C4 RA 23 83.800 65.480 5.140 1.00 0.00
+ATOM 719 C3' RA 23 82.960 65.070 0.880 1.00 0.00
+ATOM 720 H3' RA 23 84.040 65.070 0.830 1.00 0.00
+ATOM 721 C2' RA 23 82.690 65.740 2.230 1.00 0.00
+ATOM 722 1H2' RA 23 83.610 66.250 2.490 1.00 0.00
+ATOM 723 O2' RA 23 81.610 66.640 2.290 1.00 0.00
+ATOM 724 2HO' RA 23 80.820 66.110 2.370 1.00 0.00
+ATOM 725 O3' RA 23 82.400 65.840 -0.160 1.00 0.00
+ATOM 726 P RU 24 82.700 65.520 -1.710 1.00 0.00
+ATOM 727 O1P RU 24 84.090 65.020 -1.840 1.00 0.00
+ATOM 728 O2P RU 24 82.300 66.720 -2.490 1.00 0.00
+ATOM 729 O5' RU 24 81.740 64.290 -2.100 1.00 0.00
+ATOM 730 C5' RU 24 80.330 64.260 -2.090 1.00 0.00
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+ATOM 732 2H5' RU 24 79.870 64.450 -1.120 1.00 0.00
+ATOM 733 C4' RU 24 79.820 62.960 -2.690 1.00 0.00
+ATOM 734 H4' RU 24 78.730 62.910 -2.740 1.00 0.00
+ATOM 735 O4' RU 24 80.210 62.930 -4.040 1.00 0.00
+ATOM 736 C1' RU 24 80.980 61.770 -4.250 1.00 0.00
+ATOM 737 H1' RU 24 80.200 61.080 -4.540 1.00 0.00
+ATOM 738 N1 RU 24 82.030 62.090 -5.240 1.00 0.00
+ATOM 739 C6 RU 24 82.940 63.100 -5.090 1.00 0.00
+ATOM 740 H6 RU 24 82.870 63.700 -4.190 1.00 0.00
+ATOM 741 C5 RU 24 83.870 63.300 -6.050 1.00 0.00
+ATOM 742 H5 RU 24 84.610 64.070 -5.920 1.00 0.00
+ATOM 743 C4 RU 24 84.090 62.370 -7.130 1.00 0.00
+ATOM 744 O4 RU 24 85.020 62.390 -7.940 1.00 0.00
+ATOM 745 N3 RU 24 83.050 61.460 -7.300 1.00 0.00
+ATOM 746 H3 RU 24 83.280 60.740 -7.970 1.00 0.00
+ATOM 747 C2 RU 24 82.010 61.330 -6.390 1.00 0.00
+ATOM 748 O2 RU 24 81.050 60.620 -6.700 1.00 0.00
+ATOM 749 C3' RU 24 80.330 61.690 -2.010 1.00 0.00
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+ATOM 751 C2' RU 24 81.550 61.420 -2.880 1.00 0.00
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+ATOM 754 2HO' RU 24 81.120 59.550 -2.420 1.00 0.00
+ATOM 755 O3' RU 24 79.280 60.750 -2.120 1.00 0.00
+ATOM 756 P RG 25 78.100 60.720 -1.030 1.00 0.00
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+ATOM 759 O5' RG 25 78.840 60.280 0.330 1.00 0.00
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+ATOM 761 1H5' RG 25 80.160 58.730 -0.030 1.00 0.00
+ATOM 762 2H5' RG 25 78.600 58.190 0.250 1.00 0.00
+ATOM 763 C4' RG 25 79.810 58.660 1.980 1.00 0.00
+ATOM 764 H4' RG 25 80.240 57.670 1.860 1.00 0.00
+ATOM 765 O4' RG 25 80.820 59.600 2.290 1.00 0.00
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+ATOM 767 H1' RG 25 81.750 59.740 4.260 1.00 0.00
+ATOM 768 N9 RG 25 80.310 61.080 4.010 1.00 0.00
+ATOM 769 C8 RG 25 79.440 61.850 3.270 1.00 0.00
+ATOM 770 H8 RG 25 79.040 61.500 2.330 1.00 0.00
+ATOM 771 N7 RG 25 79.040 62.930 3.890 1.00 0.00
+ATOM 772 C5 RG 25 79.810 62.930 5.050 1.00 0.00
+ATOM 773 C6 RG 25 79.940 63.930 6.050 1.00 0.00
+ATOM 774 O6 RG 25 79.460 65.050 6.020 1.00 0.00
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+ATOM 776 H1 RG 25 81.030 64.320 7.740 1.00 0.00
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+ATOM 778 N2 RG 25 82.510 62.250 7.960 1.00 0.00
+ATOM 779 H21 RG 25 82.660 62.950 8.680 1.00 0.00
+ATOM 780 H22 RG 25 83.270 61.630 7.730 1.00 0.00
+ATOM 781 N3 RG 25 81.490 61.490 6.070 1.00 0.00
+ATOM 782 C4 RG 25 80.510 61.760 5.180 1.00 0.00
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+ATOM 784 H3' RG 25 78.270 59.530 3.240 1.00 0.00
+ATOM 785 C2' RG 25 79.910 58.680 4.300 1.00 0.00
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+ATOM 788 2HO' RG 25 81.150 57.520 5.260 1.00 0.00
+ATOM 789 O3' RG 25 78.050 57.480 3.080 1.00 0.00
+ATOM 790 P RG 26 76.640 57.430 3.870 1.00 0.00
+ATOM 791 O1P RG 26 76.150 56.040 3.680 1.00 0.00
+ATOM 792 O2P RG 26 75.850 58.580 3.390 1.00 0.00
+ATOM 793 O5' RG 26 77.050 57.730 5.400 1.00 0.00
+ATOM 794 C5' RG 26 77.730 56.770 6.170 1.00 0.00
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+ATOM 796 2H5' RG 26 77.050 55.920 6.250 1.00 0.00
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+ATOM 870 H5 RU 28 75.050 49.370 11.890 1.00 0.00
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+ATOM 884 P RU 29 70.100 45.310 9.820 1.00 0.00
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+ATOM 1197 C3' RC 38 53.280 40.870 26.430 1.00 0.00
+ATOM 1198 H3' RC 38 54.110 41.560 26.580 1.00 0.00
+ATOM 1199 C2' RC 38 52.000 41.610 26.040 1.00 0.00
+ATOM 1200 1H2' RC 38 52.100 42.320 25.220 1.00 0.00
+ATOM 1201 O2' RC 38 50.960 40.690 25.800 1.00 0.00
+ATOM 1202 2HO' RC 38 51.020 40.320 24.920 1.00 0.00
+ATOM 1203 O3' RC 38 53.640 39.800 25.580 1.00 0.00
+ATOM 1204 P RU 39 54.520 40.030 24.260 1.00 0.00
+ATOM 1205 O1P RU 39 53.980 39.200 23.160 1.00 0.00
+ATOM 1206 O2P RU 39 55.950 39.860 24.610 1.00 0.00
+ATOM 1207 O5' RU 39 54.250 41.580 23.900 1.00 0.00
+ATOM 1208 C5' RU 39 53.300 42.000 22.950 1.00 0.00
+ATOM 1209 1H5' RU 39 52.320 41.610 23.220 1.00 0.00
+ATOM 1210 2H5' RU 39 53.510 41.540 21.990 1.00 0.00
+ATOM 1211 C4' RU 39 53.360 43.510 22.720 1.00 0.00
+ATOM 1212 H4' RU 39 52.650 43.840 21.960 1.00 0.00
+ATOM 1213 O4' RU 39 53.170 44.250 23.900 1.00 0.00
+ATOM 1214 C1' RU 39 54.000 45.400 23.870 1.00 0.00
+ATOM 1215 H1' RU 39 53.380 46.290 23.940 1.00 0.00
+ATOM 1216 N1 RU 39 54.890 45.520 25.040 1.00 0.00
+ATOM 1217 C6 RU 39 55.230 44.420 25.770 1.00 0.00
+ATOM 1218 H6 RU 39 54.840 43.480 25.390 1.00 0.00
+ATOM 1219 C5 RU 39 55.920 44.530 26.920 1.00 0.00
+ATOM 1220 H5 RU 39 56.140 43.680 27.550 1.00 0.00
+ATOM 1221 C4 RU 39 56.300 45.810 27.480 1.00 0.00
+ATOM 1222 O4 RU 39 56.970 46.020 28.490 1.00 0.00
+ATOM 1223 N3 RU 39 55.980 46.850 26.620 1.00 0.00
+ATOM 1224 H3 RU 39 56.150 47.760 27.010 1.00 0.00
+ATOM 1225 C2 RU 39 55.160 46.790 25.500 1.00 0.00
+ATOM 1226 O2 RU 39 54.800 47.830 24.940 1.00 0.00
+ATOM 1227 C3' RU 39 54.730 43.870 22.160 1.00 0.00
+ATOM 1228 H3' RU 39 55.530 43.490 22.790 1.00 0.00
+ATOM 1229 C2' RU 39 54.760 45.350 22.550 1.00 0.00
+ATOM 1230 1H2' RU 39 55.760 45.720 22.790 1.00 0.00
+ATOM 1231 O2' RU 39 54.140 46.180 21.590 1.00 0.00
+ATOM 1232 2HO' RU 39 54.410 47.100 21.590 1.00 0.00
+ATOM 1233 O3' RU 39 54.940 43.490 20.820 1.00 0.00
+ATOM 1234 P RA 40 56.430 43.550 20.200 1.00 0.00
+ATOM 1235 O1P RA 40 56.480 43.180 18.770 1.00 0.00
+ATOM 1236 O2P RA 40 57.340 42.900 21.170 1.00 0.00
+ATOM 1237 O5' RA 40 56.770 45.120 20.290 1.00 0.00
+ATOM 1238 C5' RA 40 56.260 45.960 19.280 1.00 0.00
+ATOM 1239 1H5' RA 40 55.170 45.960 19.240 1.00 0.00
+ATOM 1240 2H5' RA 40 56.700 45.780 18.300 1.00 0.00
+ATOM 1241 C4' RA 40 56.630 47.400 19.610 1.00 0.00
+ATOM 1242 H4' RA 40 56.060 48.030 18.930 1.00 0.00
+ATOM 1243 O4' RA 40 56.370 47.680 20.960 1.00 0.00
+ATOM 1244 C1' RA 40 57.450 48.450 21.450 1.00 0.00
+ATOM 1245 H1' RA 40 57.000 49.410 21.700 1.00 0.00
+ATOM 1246 N9 RA 40 57.980 47.870 22.700 1.00 0.00
+ATOM 1247 C8 RA 40 58.080 46.550 23.070 1.00 0.00
+ATOM 1248 H8 RA 40 57.840 45.710 22.440 1.00 0.00
+ATOM 1249 N7 RA 40 58.420 46.430 24.330 1.00 0.00
+ATOM 1250 C5 RA 40 58.660 47.710 24.820 1.00 0.00
+ATOM 1251 C6 RA 40 59.120 48.240 26.040 1.00 0.00
+ATOM 1252 N6 RA 40 59.360 47.590 27.180 1.00 0.00
+ATOM 1253 H61 RA 40 59.180 46.590 27.210 1.00 0.00
+ATOM 1254 H62 RA 40 59.800 48.040 27.970 1.00 0.00
+ATOM 1255 N1 RA 40 59.040 49.570 26.190 1.00 0.00
+ATOM 1256 C2 RA 40 58.630 50.310 25.180 1.00 0.00
+ATOM 1257 H2 RA 40 58.530 51.370 25.360 1.00 0.00
+ATOM 1258 N3 RA 40 58.330 49.930 23.950 1.00 0.00
+ATOM 1259 C4 RA 40 58.330 48.580 23.820 1.00 0.00
+ATOM 1260 C3' RA 40 58.090 47.770 19.360 1.00 0.00
+ATOM 1261 H3' RA 40 58.690 46.880 19.560 1.00 0.00
+ATOM 1262 C2' RA 40 58.530 48.770 20.420 1.00 0.00
+ATOM 1263 1H2' RA 40 59.550 48.600 20.770 1.00 0.00
+ATOM 1264 O2' RA 40 58.340 50.130 20.100 1.00 0.00
+ATOM 1265 2HO' RA 40 59.170 50.620 20.040 1.00 0.00
+ATOM 1266 O3' RA 40 58.220 48.280 18.050 1.00 0.00
+ATOM 1267 P RC 41 59.690 48.450 17.410 1.00 0.00
+ATOM 1268 O1P RC 41 59.510 49.060 16.070 1.00 0.00
+ATOM 1269 O2P RC 41 60.300 47.110 17.350 1.00 0.00
+ATOM 1270 O5' RC 41 60.720 49.400 18.210 1.00 0.00
+ATOM 1271 C5' RC 41 60.490 50.790 18.140 1.00 0.00
+ATOM 1272 1H5' RC 41 59.430 51.060 18.130 1.00 0.00
+ATOM 1273 2H5' RC 41 60.880 51.140 17.180 1.00 0.00
+ATOM 1274 C4' RC 41 61.180 51.520 19.280 1.00 0.00
+ATOM 1275 H4' RC 41 60.890 52.570 19.200 1.00 0.00
+ATOM 1276 O4' RC 41 60.770 51.020 20.530 1.00 0.00
+ATOM 1277 C1' RC 41 61.870 50.940 21.410 1.00 0.00
+ATOM 1278 H1' RC 41 61.740 51.760 22.120 1.00 0.00
+ATOM 1279 N1 RC 41 62.020 49.640 22.100 1.00 0.00
+ATOM 1280 C6 RC 41 62.000 48.510 21.330 1.00 0.00
+ATOM 1281 H6 RC 41 62.230 48.680 20.290 1.00 0.00
+ATOM 1282 C5 RC 41 61.920 47.250 21.810 1.00 0.00
+ATOM 1283 H5 RC 41 61.950 46.340 21.230 1.00 0.00
+ATOM 1284 C4 RC 41 61.820 47.130 23.230 1.00 0.00
+ATOM 1285 N4 RC 41 61.790 45.940 23.840 1.00 0.00
+ATOM 1286 H41 RC 41 61.730 45.090 23.300 1.00 0.00
+ATOM 1287 H42 RC 41 61.830 45.860 24.850 1.00 0.00
+ATOM 1288 N3 RC 41 61.850 48.200 24.040 1.00 0.00
+ATOM 1289 C2 RC 41 61.870 49.430 23.460 1.00 0.00
+ATOM 1290 O2 RC 41 61.750 50.400 24.200 1.00 0.00
+ATOM 1291 C3' RC 41 62.670 51.180 19.160 1.00 0.00
+ATOM 1292 H3' RC 41 62.860 50.120 18.990 1.00 0.00
+ATOM 1293 C2' RC 41 63.100 51.350 20.620 1.00 0.00
+ATOM 1294 1H2' RC 41 63.940 50.700 20.880 1.00 0.00
+ATOM 1295 O2' RC 41 63.330 52.690 20.980 1.00 0.00
+ATOM 1296 2HO' RC 41 64.080 53.060 20.500 1.00 0.00
+ATOM 1297 O3' RC 41 63.360 52.070 18.320 1.00 0.00
+ATOM 1298 P RC 42 64.340 51.600 17.130 1.00 0.00
+ATOM 1299 O1P RC 42 64.270 50.120 17.060 1.00 0.00
+ATOM 1300 O2P RC 42 65.670 52.230 17.170 1.00 0.00
+ATOM 1301 O5' RC 42 63.720 52.280 15.810 1.00 0.00
+ATOM 1302 C5' RC 42 62.710 51.610 15.080 1.00 0.00
+ATOM 1303 1H5' RC 42 62.050 50.980 15.680 1.00 0.00
+ATOM 1304 2H5' RC 42 63.190 51.000 14.320 1.00 0.00
+ATOM 1305 C4' RC 42 61.770 52.590 14.400 1.00 0.00
+ATOM 1306 H4' RC 42 61.060 52.120 13.710 1.00 0.00
+ATOM 1307 O4' RC 42 60.870 53.150 15.330 1.00 0.00
+ATOM 1308 C1' RC 42 60.660 54.500 14.970 1.00 0.00
+ATOM 1309 H1' RC 42 59.610 54.730 14.810 1.00 0.00
+ATOM 1310 N1 RC 42 61.200 55.440 15.960 1.00 0.00
+ATOM 1311 C6 RC 42 62.020 55.060 16.980 1.00 0.00
+ATOM 1312 H6 RC 42 62.170 54.000 17.160 1.00 0.00
+ATOM 1313 C5 RC 42 62.420 55.960 17.900 1.00 0.00
+ATOM 1314 H5 RC 42 62.900 55.590 18.800 1.00 0.00
+ATOM 1315 C4 RC 42 62.140 57.340 17.650 1.00 0.00
+ATOM 1316 N4 RC 42 62.550 58.250 18.550 1.00 0.00
+ATOM 1317 H41 RC 42 63.130 57.950 19.320 1.00 0.00
+ATOM 1318 H42 RC 42 62.240 59.210 18.470 1.00 0.00
+ATOM 1319 N3 RC 42 61.340 57.720 16.650 1.00 0.00
+ATOM 1320 C2 RC 42 60.850 56.770 15.800 1.00 0.00
+ATOM 1321 O2 RC 42 60.060 57.170 14.950 1.00 0.00
+ATOM 1322 C3' RC 42 62.480 53.720 13.670 1.00 0.00
+ATOM 1323 H3' RC 42 63.260 54.050 14.350 1.00 0.00
+ATOM 1324 C2' RC 42 61.310 54.690 13.600 1.00 0.00
+ATOM 1325 1H2' RC 42 61.710 55.700 13.550 1.00 0.00
+ATOM 1326 O2' RC 42 60.350 54.370 12.610 1.00 0.00
+ATOM 1327 2HO' RC 42 60.660 54.600 11.730 1.00 0.00
+ATOM 1328 O3' RC 42 62.950 53.550 12.350 1.00 0.00
+ATOM 1329 P RA 43 64.150 54.480 11.800 1.00 0.00
+ATOM 1330 O1P RA 43 64.850 53.660 10.800 1.00 0.00
+ATOM 1331 O2P RA 43 64.940 54.980 12.950 1.00 0.00
+ATOM 1332 O5' RA 43 63.470 55.740 11.060 1.00 0.00
+ATOM 1333 C5' RA 43 62.540 55.580 10.010 1.00 0.00
+ATOM 1334 1H5' RA 43 61.870 54.740 10.180 1.00 0.00
+ATOM 1335 2H5' RA 43 63.090 55.360 9.100 1.00 0.00
+ATOM 1336 C4' RA 43 61.710 56.860 9.900 1.00 0.00
+ATOM 1337 H4' RA 43 60.900 56.660 9.200 1.00 0.00
+ATOM 1338 O4' RA 43 61.110 57.150 11.150 1.00 0.00
+ATOM 1339 C1' RA 43 61.100 58.550 11.280 1.00 0.00
+ATOM 1340 H1' RA 43 60.130 58.910 11.620 1.00 0.00
+ATOM 1341 N9 RA 43 61.990 59.100 12.310 1.00 0.00
+ATOM 1342 C8 RA 43 62.940 58.470 13.070 1.00 0.00
+ATOM 1343 H8 RA 43 63.240 57.450 12.890 1.00 0.00
+ATOM 1344 N7 RA 43 63.480 59.200 14.010 1.00 0.00
+ATOM 1345 C5 RA 43 62.760 60.390 13.980 1.00 0.00
+ATOM 1346 C6 RA 43 62.730 61.530 14.800 1.00 0.00
+ATOM 1347 N6 RA 43 63.680 61.650 15.740 1.00 0.00
+ATOM 1348 H61 RA 43 64.370 60.930 15.850 1.00 0.00
+ATOM 1349 H62 RA 43 63.790 62.560 16.170 1.00 0.00
+ATOM 1350 N1 RA 43 61.800 62.480 14.660 1.00 0.00
+ATOM 1351 C2 RA 43 61.030 62.320 13.590 1.00 0.00
+ATOM 1352 H2 RA 43 60.390 63.170 13.420 1.00 0.00
+ATOM 1353 N3 RA 43 60.960 61.300 12.750 1.00 0.00
+ATOM 1354 C4 RA 43 61.850 60.300 12.960 1.00 0.00
+ATOM 1355 C3' RA 43 62.450 58.110 9.430 1.00 0.00
+ATOM 1356 H3' RA 43 63.410 58.140 9.940 1.00 0.00
+ATOM 1357 C2' RA 43 61.520 59.200 9.960 1.00 0.00
+ATOM 1358 1H2' RA 43 62.100 60.100 10.180 1.00 0.00
+ATOM 1359 O2' RA 43 60.360 59.510 9.220 1.00 0.00
+ATOM 1360 2HO' RA 43 60.020 60.280 9.690 1.00 0.00
+ATOM 1361 O3' RA 43 62.720 58.060 8.050 1.00 0.00
+ATOM 1362 P RA 44 63.840 59.010 7.380 1.00 0.00
+ATOM 1363 O1P RA 44 63.650 58.990 5.910 1.00 0.00
+ATOM 1364 O2P RA 44 65.130 58.520 7.890 1.00 0.00
+ATOM 1365 O5' RA 44 63.590 60.510 7.920 1.00 0.00
+ATOM 1366 C5' RA 44 62.650 61.310 7.240 1.00 0.00
+ATOM 1367 1H5' RA 44 61.690 60.850 7.000 1.00 0.00
+ATOM 1368 2H5' RA 44 62.990 61.670 6.270 1.00 0.00
+ATOM 1369 C4' RA 44 62.260 62.620 7.910 1.00 0.00
+ATOM 1370 H4' RA 44 61.470 63.110 7.340 1.00 0.00
+ATOM 1371 O4' RA 44 61.760 62.600 9.230 1.00 0.00
+ATOM 1372 C1' RA 44 62.230 63.710 9.950 1.00 0.00
+ATOM 1373 H1' RA 44 61.440 64.220 10.510 1.00 0.00
+ATOM 1374 N9 RA 44 63.240 63.260 10.920 1.00 0.00
+ATOM 1375 C8 RA 44 63.950 62.090 11.070 1.00 0.00
+ATOM 1376 H8 RA 44 64.010 61.350 10.290 1.00 0.00
+ATOM 1377 N7 RA 44 64.760 62.060 12.100 1.00 0.00
+ATOM 1378 C5 RA 44 64.480 63.290 12.690 1.00 0.00
+ATOM 1379 C6 RA 44 64.930 64.010 13.810 1.00 0.00
+ATOM 1380 N6 RA 44 65.760 63.450 14.700 1.00 0.00
+ATOM 1381 H61 RA 44 66.240 62.570 14.550 1.00 0.00
+ATOM 1382 H62 RA 44 66.120 64.090 15.390 1.00 0.00
+ATOM 1383 N1 RA 44 64.550 65.260 14.110 1.00 0.00
+ATOM 1384 C2 RA 44 63.620 65.800 13.340 1.00 0.00
+ATOM 1385 H2 RA 44 63.270 66.770 13.680 1.00 0.00
+ATOM 1386 N3 RA 44 63.010 65.240 12.320 1.00 0.00
+ATOM 1387 C4 RA 44 63.550 64.040 12.010 1.00 0.00
+ATOM 1388 C3' RA 44 63.400 63.640 7.970 1.00 0.00
+ATOM 1389 H3' RA 44 64.320 63.300 8.450 1.00 0.00
+ATOM 1390 C2' RA 44 62.870 64.670 8.960 1.00 0.00
+ATOM 1391 1H2' RA 44 63.710 65.210 9.400 1.00 0.00
+ATOM 1392 O2' RA 44 61.890 65.580 8.510 1.00 0.00
+ATOM 1393 2HO' RA 44 62.320 66.440 8.540 1.00 0.00
+ATOM 1394 O3' RA 44 63.580 64.160 6.670 1.00 0.00
+ATOM 1395 P RG 45 65.030 64.700 6.220 1.00 0.00
+ATOM 1396 O1P RG 45 65.080 65.130 4.810 1.00 0.00
+ATOM 1397 O2P RG 45 66.040 63.730 6.720 1.00 0.00
+ATOM 1398 O5' RG 45 65.120 66.030 7.120 1.00 0.00
+ATOM 1399 C5' RG 45 64.340 67.160 6.780 1.00 0.00
+ATOM 1400 1H5' RG 45 63.420 66.800 6.320 1.00 0.00
+ATOM 1401 2H5' RG 45 64.840 67.760 6.020 1.00 0.00
+ATOM 1402 C4' RG 45 64.180 68.190 7.880 1.00 0.00
+ATOM 1403 H4' RG 45 63.350 68.850 7.620 1.00 0.00
+ATOM 1404 O4' RG 45 63.910 67.630 9.150 1.00 0.00
+ATOM 1405 C1' RG 45 64.720 68.180 10.170 1.00 0.00
+ATOM 1406 H1' RG 45 64.040 68.350 11.010 1.00 0.00
+ATOM 1407 N9 RG 45 65.780 67.250 10.600 1.00 0.00
+ATOM 1408 C8 RG 45 66.110 65.990 10.180 1.00 0.00
+ATOM 1409 H8 RG 45 65.780 65.630 9.210 1.00 0.00
+ATOM 1410 N7 RG 45 66.870 65.330 11.000 1.00 0.00
+ATOM 1411 C5 RG 45 67.130 66.260 12.010 1.00 0.00
+ATOM 1412 C6 RG 45 67.960 66.090 13.150 1.00 0.00
+ATOM 1413 O6 RG 45 68.680 65.170 13.520 1.00 0.00
+ATOM 1414 N1 RG 45 68.040 67.260 13.890 1.00 0.00
+ATOM 1415 H1 RG 45 68.850 67.230 14.500 1.00 0.00
+ATOM 1416 C2 RG 45 67.440 68.460 13.540 1.00 0.00
+ATOM 1417 N2 RG 45 67.690 69.490 14.350 1.00 0.00
+ATOM 1418 H21 RG 45 68.420 69.380 15.040 1.00 0.00
+ATOM 1419 H22 RG 45 67.380 70.390 14.010 1.00 0.00
+ATOM 1420 N3 RG 45 66.710 68.610 12.430 1.00 0.00
+ATOM 1421 C4 RG 45 66.510 67.450 11.750 1.00 0.00
+ATOM 1422 C3' RG 45 65.440 69.020 8.100 1.00 0.00
+ATOM 1423 H3' RG 45 66.310 68.380 7.980 1.00 0.00
+ATOM 1424 C2' RG 45 65.240 69.470 9.540 1.00 0.00
+ATOM 1425 1H2' RG 45 66.220 69.620 9.980 1.00 0.00
+ATOM 1426 O2' RG 45 64.370 70.570 9.700 1.00 0.00
+ATOM 1427 2HO' RG 45 64.620 71.130 8.960 1.00 0.00
+ATOM 1428 O3' RG 45 65.470 70.190 7.300 1.00 0.00
+ATOM 1429 P RA 46 66.810 70.570 6.500 1.00 0.00
+ATOM 1430 O1P RA 46 66.490 71.770 5.690 1.00 0.00
+ATOM 1431 O2P RA 46 67.340 69.400 5.770 1.00 0.00
+ATOM 1432 O5' RA 46 67.800 70.980 7.710 1.00 0.00
+ATOM 1433 C5' RA 46 67.640 72.190 8.410 1.00 0.00
+ATOM 1434 1H5' RA 46 66.610 72.260 8.770 1.00 0.00
+ATOM 1435 2H5' RA 46 67.860 73.050 7.780 1.00 0.00
+ATOM 1436 C4' RA 46 68.540 72.340 9.640 1.00 0.00
+ATOM 1437 H4' RA 46 68.420 73.340 10.070 1.00 0.00
+ATOM 1438 O4' RA 46 68.220 71.350 10.590 1.00 0.00
+ATOM 1439 C1' RA 46 69.390 70.880 11.220 1.00 0.00
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+ATOM 1441 N9 RA 46 69.680 69.470 10.930 1.00 0.00
+ATOM 1442 C8 RA 46 69.180 68.620 9.980 1.00 0.00
+ATOM 1443 H8 RA 46 68.540 68.860 9.150 1.00 0.00
+ATOM 1444 N7 RA 46 69.670 67.410 9.980 1.00 0.00
+ATOM 1445 C5 RA 46 70.430 67.410 11.150 1.00 0.00
+ATOM 1446 C6 RA 46 71.180 66.470 11.870 1.00 0.00
+ATOM 1447 N6 RA 46 71.330 65.180 11.560 1.00 0.00
+ATOM 1448 H61 RA 46 70.910 64.950 10.670 1.00 0.00
+ATOM 1449 H62 RA 46 71.840 64.530 12.140 1.00 0.00
+ATOM 1450 N1 RA 46 71.740 66.740 13.060 1.00 0.00
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+ATOM 1452 H2 RA 46 72.110 68.190 14.450 1.00 0.00
+ATOM 1453 N3 RA 46 70.940 68.970 12.950 1.00 0.00
+ATOM 1454 C4 RA 46 70.400 68.640 11.760 1.00 0.00
+ATOM 1455 C3' RA 46 70.030 72.200 9.370 1.00 0.00
+ATOM 1456 H3' RA 46 70.090 71.310 8.740 1.00 0.00
+ATOM 1457 C2' RA 46 70.530 71.780 10.750 1.00 0.00
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+ATOM 1459 O2' RA 46 70.630 72.930 11.550 1.00 0.00
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+ATOM 1461 O3' RA 46 70.630 73.350 8.800 1.00 0.00
+ATOM 1462 P RG 47 72.210 73.480 8.490 1.00 0.00
+ATOM 1463 O1P RG 47 72.380 74.780 7.790 1.00 0.00
+ATOM 1464 O2P RG 47 72.640 72.230 7.820 1.00 0.00
+ATOM 1465 O5' RG 47 72.910 73.430 9.930 1.00 0.00
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+ATOM 1467 1H5' RG 47 74.780 74.320 9.600 1.00 0.00
+ATOM 1468 2H5' RG 47 74.700 72.550 9.560 1.00 0.00
+ATOM 1469 C4' RG 47 74.500 73.270 11.550 1.00 0.00
+ATOM 1470 H4' RG 47 74.360 74.250 12.000 1.00 0.00
+ATOM 1471 O4' RG 47 73.610 72.330 12.120 1.00 0.00
+ATOM 1472 C1' RG 47 74.300 71.280 12.760 1.00 0.00
+ATOM 1473 H1' RG 47 73.890 71.100 13.750 1.00 0.00
+ATOM 1474 N9 RG 47 74.330 70.030 11.960 1.00 0.00
+ATOM 1475 C8 RG 47 73.880 69.790 10.690 1.00 0.00
+ATOM 1476 H8 RG 47 73.570 70.530 9.970 1.00 0.00
+ATOM 1477 N7 RG 47 73.980 68.520 10.410 1.00 0.00
+ATOM 1478 C5 RG 47 74.680 67.940 11.460 1.00 0.00
+ATOM 1479 C6 RG 47 75.110 66.600 11.680 1.00 0.00
+ATOM 1480 O6 RG 47 74.950 65.590 11.000 1.00 0.00
+ATOM 1481 N1 RG 47 75.650 66.440 12.950 1.00 0.00
+ATOM 1482 H1 RG 47 76.020 65.540 13.230 1.00 0.00
+ATOM 1483 C2 RG 47 75.950 67.460 13.830 1.00 0.00
+ATOM 1484 N2 RG 47 76.710 67.210 14.900 1.00 0.00
+ATOM 1485 H21 RG 47 77.220 66.350 15.060 1.00 0.00
+ATOM 1486 H22 RG 47 76.980 68.010 15.450 1.00 0.00
+ATOM 1487 N3 RG 47 75.600 68.730 13.580 1.00 0.00
+ATOM 1488 C4 RG 47 74.980 68.900 12.390 1.00 0.00
+ATOM 1489 C3' RG 47 75.900 72.830 11.950 1.00 0.00
+ATOM 1490 H3' RG 47 76.490 72.330 11.180 1.00 0.00
+ATOM 1491 C2' RG 47 75.660 71.860 13.110 1.00 0.00
+ATOM 1492 1H2' RG 47 76.490 71.160 13.170 1.00 0.00
+ATOM 1493 O2' RG 47 75.570 72.560 14.330 1.00 0.00
+ATOM 1494 2HO' RG 47 75.900 73.430 14.090 1.00 0.00
+ATOM 1495 O3' RG 47 76.680 73.890 12.450 1.00 0.00
+ATOM 1496 P RC 48 78.240 74.020 12.040 1.00 0.00
+ATOM 1497 O1P RC 48 78.860 75.190 12.690 1.00 0.00
+ATOM 1498 O2P RC 48 78.260 74.020 10.560 1.00 0.00
+ATOM 1499 O5' RC 48 78.900 72.680 12.630 1.00 0.00
+ATOM 1500 C5' RC 48 79.350 72.580 13.970 1.00 0.00
+ATOM 1501 1H5' RC 48 78.590 72.760 14.730 1.00 0.00
+ATOM 1502 2H5' RC 48 80.130 73.310 14.170 1.00 0.00
+ATOM 1503 C4' RC 48 79.790 71.130 14.140 1.00 0.00
+ATOM 1504 H4' RC 48 80.130 70.970 15.160 1.00 0.00
+ATOM 1505 O4' RC 48 78.820 70.160 13.820 1.00 0.00
+ATOM 1506 C1' RC 48 79.330 69.040 13.130 1.00 0.00
+ATOM 1507 H1' RC 48 79.110 68.140 13.710 1.00 0.00
+ATOM 1508 N1 RC 48 78.810 68.850 11.770 1.00 0.00
+ATOM 1509 C6 RC 48 78.150 69.810 11.070 1.00 0.00
+ATOM 1510 H6 RC 48 78.210 70.870 11.260 1.00 0.00
+ATOM 1511 C5 RC 48 77.350 69.460 10.040 1.00 0.00
+ATOM 1512 H5 RC 48 76.820 70.220 9.480 1.00 0.00
+ATOM 1513 C4 RC 48 77.310 68.090 9.620 1.00 0.00
+ATOM 1514 N4 RC 48 76.670 67.780 8.490 1.00 0.00
+ATOM 1515 H41 RC 48 76.260 68.530 7.950 1.00 0.00
+ATOM 1516 H42 RC 48 76.790 66.850 8.120 1.00 0.00
+ATOM 1517 N3 RC 48 78.100 67.190 10.220 1.00 0.00
+ATOM 1518 C2 RC 48 78.860 67.550 11.290 1.00 0.00
+ATOM 1519 O2 RC 48 79.500 66.610 11.750 1.00 0.00
+ATOM 1520 C3' RC 48 80.970 70.740 13.260 1.00 0.00
+ATOM 1521 H3' RC 48 80.940 71.210 12.280 1.00 0.00
+ATOM 1522 C2' RC 48 80.850 69.220 13.120 1.00 0.00
+ATOM 1523 1H2' RC 48 81.370 68.840 12.240 1.00 0.00
+ATOM 1524 O2' RC 48 81.400 68.500 14.200 1.00 0.00
+ATOM 1525 2HO' RC 48 82.130 69.020 14.550 1.00 0.00
+ATOM 1526 O3' RC 48 82.170 71.180 13.850 1.00 0.00
+ATOM 1527 P RC 49 83.480 71.590 13.010 1.00 0.00
+ATOM 1528 O1P RC 49 84.460 72.150 13.960 1.00 0.00
+ATOM 1529 O2P RC 49 83.100 72.380 11.810 1.00 0.00
+ATOM 1530 O5' RC 49 84.090 70.180 12.530 1.00 0.00
+ATOM 1531 C5' RC 49 84.640 69.300 13.480 1.00 0.00
+ATOM 1532 1H5' RC 49 83.970 69.190 14.330 1.00 0.00
+ATOM 1533 2H5' RC 49 85.480 69.830 13.920 1.00 0.00
+ATOM 1534 C4' RC 49 84.960 67.980 12.790 1.00 0.00
+ATOM 1535 H4' RC 49 85.400 67.340 13.560 1.00 0.00
+ATOM 1536 O4' RC 49 83.750 67.470 12.280 1.00 0.00
+ATOM 1537 C1' RC 49 83.950 66.670 11.140 1.00 0.00
+ATOM 1538 H1' RC 49 84.060 65.610 11.390 1.00 0.00
+ATOM 1539 N1 RC 49 82.870 66.880 10.150 1.00 0.00
+ATOM 1540 C6 RC 49 82.470 68.130 9.800 1.00 0.00
+ATOM 1541 H6 RC 49 83.030 68.890 10.320 1.00 0.00
+ATOM 1542 C5 RC 49 81.570 68.380 8.820 1.00 0.00
+ATOM 1543 H5 RC 49 81.270 69.410 8.660 1.00 0.00
+ATOM 1544 C4 RC 49 81.110 67.200 8.160 1.00 0.00
+ATOM 1545 N4 RC 49 80.200 67.440 7.200 1.00 0.00
+ATOM 1546 H41 RC 49 79.750 68.340 7.140 1.00 0.00
+ATOM 1547 H42 RC 49 79.630 66.630 7.000 1.00 0.00
+ATOM 1548 N3 RC 49 81.550 65.950 8.370 1.00 0.00
+ATOM 1549 C2 RC 49 82.470 65.820 9.360 1.00 0.00
+ATOM 1550 O2 RC 49 82.920 64.690 9.560 1.00 0.00
+ATOM 1551 C3' RC 49 85.900 68.160 11.600 1.00 0.00
+ATOM 1552 H3' RC 49 85.700 69.140 11.180 1.00 0.00
+ATOM 1553 C2' RC 49 85.340 67.080 10.680 1.00 0.00
+ATOM 1554 1H2' RC 49 85.270 67.490 9.670 1.00 0.00
+ATOM 1555 O2' RC 49 86.240 66.000 10.770 1.00 0.00
+ATOM 1556 2HO' RC 49 85.880 65.170 11.080 1.00 0.00
+ATOM 1557 O3' RC 49 87.230 67.990 12.060 1.00 0.00
+ATOM 1558 P RU 50 88.360 69.130 11.970 1.00 0.00
+ATOM 1559 O1P RU 50 89.610 68.640 12.570 1.00 0.00
+ATOM 1560 O2P RU 50 87.840 70.420 12.480 1.00 0.00
+ATOM 1561 O5' RU 50 88.710 69.260 10.400 1.00 0.00
+ATOM 1562 C5' RU 50 89.170 68.160 9.650 1.00 0.00
+ATOM 1563 1H5' RU 50 88.630 67.250 9.910 1.00 0.00
+ATOM 1564 2H5' RU 50 90.190 67.980 9.990 1.00 0.00
+ATOM 1565 C4' RU 50 89.150 68.240 8.120 1.00 0.00
+ATOM 1566 H4' RU 50 89.650 67.340 7.780 1.00 0.00
+ATOM 1567 O4' RU 50 87.800 68.260 7.720 1.00 0.00
+ATOM 1568 C1' RU 50 87.520 69.450 7.030 1.00 0.00
+ATOM 1569 H1' RU 50 87.630 69.210 5.970 1.00 0.00
+ATOM 1570 N1 RU 50 86.150 69.990 7.190 1.00 0.00
+ATOM 1571 C6 RU 50 85.610 70.120 8.440 1.00 0.00
+ATOM 1572 H6 RU 50 86.190 69.830 9.300 1.00 0.00
+ATOM 1573 C5 RU 50 84.330 70.510 8.630 1.00 0.00
+ATOM 1574 H5 RU 50 83.970 70.650 9.640 1.00 0.00
+ATOM 1575 C4 RU 50 83.500 70.840 7.500 1.00 0.00
+ATOM 1576 O4 RU 50 82.350 71.290 7.560 1.00 0.00
+ATOM 1577 N3 RU 50 84.090 70.690 6.250 1.00 0.00
+ATOM 1578 H3 RU 50 83.690 71.250 5.520 1.00 0.00
+ATOM 1579 C2 RU 50 85.390 70.260 6.070 1.00 0.00
+ATOM 1580 O2 RU 50 85.720 70.000 4.910 1.00 0.00
+ATOM 1581 C3' RU 50 89.840 69.530 7.680 1.00 0.00
+ATOM 1582 H3' RU 50 90.510 69.960 8.430 1.00 0.00
+ATOM 1583 C2' RU 50 88.630 70.420 7.420 1.00 0.00
+ATOM 1584 1H2' RU 50 88.390 70.960 8.330 1.00 0.00
+ATOM 1585 O2' RU 50 88.790 71.410 6.430 1.00 0.00
+ATOM 1586 2HO' RU 50 89.130 71.020 5.620 1.00 0.00
+ATOM 1587 O3' RU 50 90.470 69.390 6.430 1.00 0.00
+ATOM 1588 P RU 51 91.890 68.640 6.300 1.00 0.00
+ATOM 1589 O1P RU 51 92.770 69.110 7.390 1.00 0.00
+ATOM 1590 O2P RU 51 92.400 68.880 4.930 1.00 0.00
+ATOM 1591 O5' RU 51 91.740 67.040 6.320 1.00 0.00
+ATOM 1592 C5' RU 51 92.220 66.230 7.380 1.00 0.00
+ATOM 1593 1H5' RU 51 91.650 66.520 8.260 1.00 0.00
+ATOM 1594 2H5' RU 51 93.290 66.360 7.520 1.00 0.00
+ATOM 1595 C4' RU 51 92.040 64.740 7.110 1.00 0.00
+ATOM 1596 H4' RU 51 92.220 64.210 8.040 1.00 0.00
+ATOM 1597 O4' RU 51 90.670 64.600 6.790 1.00 0.00
+ATOM 1598 C1' RU 51 90.520 63.900 5.570 1.00 0.00
+ATOM 1599 H1' RU 51 90.280 62.910 5.960 1.00 0.00
+ATOM 1600 N1 RU 51 89.340 64.320 4.790 1.00 0.00
+ATOM 1601 C6 RU 51 88.930 65.620 4.780 1.00 0.00
+ATOM 1602 H6 RU 51 89.450 66.400 5.320 1.00 0.00
+ATOM 1603 C5 RU 51 87.920 65.950 3.950 1.00 0.00
+ATOM 1604 H5 RU 51 87.720 67.000 3.770 1.00 0.00
+ATOM 1605 C4 RU 51 87.180 65.060 3.090 1.00 0.00
+ATOM 1606 O4 RU 51 86.300 65.400 2.310 1.00 0.00
+ATOM 1607 N3 RU 51 87.500 63.720 3.320 1.00 0.00
+ATOM 1608 H3 RU 51 86.930 62.980 2.940 1.00 0.00
+ATOM 1609 C2 RU 51 88.600 63.380 4.090 1.00 0.00
+ATOM 1610 O2 RU 51 88.870 62.180 4.160 1.00 0.00
+ATOM 1611 C3' RU 51 92.820 64.170 5.930 1.00 0.00
+ATOM 1612 H3' RU 51 93.440 64.990 5.560 1.00 0.00
+ATOM 1613 C2' RU 51 91.830 63.990 4.790 1.00 0.00
+ATOM 1614 1H2' RU 51 91.950 64.880 4.180 1.00 0.00
+ATOM 1615 O2' RU 51 92.200 62.930 3.930 1.00 0.00
+ATOM 1616 2HO' RU 51 93.130 62.810 3.730 1.00 0.00
+ATOM 1617 O3' RU 51 93.500 62.970 6.250 1.00 0.00
+ATOM 1618 P RA 52 94.710 62.990 7.310 1.00 0.00
+ATOM 1619 O1P RA 52 95.440 64.270 7.200 1.00 0.00
+ATOM 1620 O2P RA 52 95.430 61.720 7.070 1.00 0.00
+ATOM 1621 O5' RA 52 94.070 63.030 8.790 1.00 0.00
+ATOM 1622 C5' RA 52 93.420 61.950 9.430 1.00 0.00
+ATOM 1623 1H5' RA 52 94.060 61.070 9.380 1.00 0.00
+ATOM 1624 2H5' RA 52 92.620 61.730 8.720 1.00 0.00
+ATOM 1625 C4' RA 52 92.830 62.410 10.760 1.00 0.00
+ATOM 1626 H4' RA 52 93.700 62.760 11.330 1.00 0.00
+ATOM 1627 O4' RA 52 91.970 63.530 10.760 1.00 0.00
+ATOM 1628 C1' RA 52 90.710 63.050 11.150 1.00 0.00
+ATOM 1629 H1' RA 52 90.320 63.820 11.810 1.00 0.00
+ATOM 1630 N9 RA 52 89.790 63.010 9.990 1.00 0.00
+ATOM 1631 C8 RA 52 88.900 63.990 9.650 1.00 0.00
+ATOM 1632 H8 RA 52 88.900 64.950 10.140 1.00 0.00
+ATOM 1633 N7 RA 52 88.090 63.730 8.660 1.00 0.00
+ATOM 1634 C5 RA 52 88.590 62.480 8.310 1.00 0.00
+ATOM 1635 C6 RA 52 88.160 61.560 7.340 1.00 0.00
+ATOM 1636 N6 RA 52 87.100 61.660 6.520 1.00 0.00
+ATOM 1637 H61 RA 52 86.520 62.470 6.390 1.00 0.00
+ATOM 1638 H62 RA 52 87.050 60.980 5.780 1.00 0.00
+ATOM 1639 N1 RA 52 88.770 60.380 7.160 1.00 0.00
+ATOM 1640 C2 RA 52 89.810 60.090 7.920 1.00 0.00
+ATOM 1641 H2 RA 52 90.270 59.160 7.600 1.00 0.00
+ATOM 1642 N3 RA 52 90.280 60.830 8.910 1.00 0.00
+ATOM 1643 C4 RA 52 89.610 61.990 9.080 1.00 0.00
+ATOM 1644 C3' RA 52 92.260 61.190 11.480 1.00 0.00
+ATOM 1645 H3' RA 52 92.150 60.360 10.790 1.00 0.00
+ATOM 1646 C2' RA 52 90.920 61.760 11.930 1.00 0.00
+ATOM 1647 1H2' RA 52 90.150 61.050 11.630 1.00 0.00
+ATOM 1648 O2' RA 52 90.810 62.220 13.260 1.00 0.00
+ATOM 1649 2HO' RA 52 90.330 61.570 13.790 1.00 0.00
+ATOM 1650 O3' RA 52 93.080 60.810 12.570 1.00 0.00
+ATOM 1651 P RA 53 92.910 59.300 13.100 1.00 0.00
+ATOM 1652 O1P RA 53 93.960 59.150 14.130 1.00 0.00
+ATOM 1653 O2P RA 53 92.830 58.320 11.990 1.00 0.00
+ATOM 1654 O5' RA 53 91.430 59.240 13.740 1.00 0.00
+ATOM 1655 C5' RA 53 91.100 59.710 15.020 1.00 0.00
+ATOM 1656 1H5' RA 53 91.500 60.720 15.080 1.00 0.00
+ATOM 1657 2H5' RA 53 91.710 59.150 15.730 1.00 0.00
+ATOM 1658 C4' RA 53 89.620 59.690 15.380 1.00 0.00
+ATOM 1659 H4' RA 53 89.560 60.140 16.370 1.00 0.00
+ATOM 1660 O4' RA 53 89.040 60.460 14.360 1.00 0.00
+ATOM 1661 C1' RA 53 87.810 59.860 14.010 1.00 0.00
+ATOM 1662 H1' RA 53 87.080 60.010 14.810 1.00 0.00
+ATOM 1663 N9 RA 53 87.260 60.350 12.730 1.00 0.00
+ATOM 1664 C8 RA 53 87.200 59.650 11.550 1.00 0.00
+ATOM 1665 H8 RA 53 87.760 58.740 11.460 1.00 0.00
+ATOM 1666 N7 RA 53 86.550 60.270 10.600 1.00 0.00
+ATOM 1667 C5 RA 53 86.170 61.500 11.130 1.00 0.00
+ATOM 1668 C6 RA 53 85.490 62.650 10.690 1.00 0.00
+ATOM 1669 N6 RA 53 85.030 62.810 9.440 1.00 0.00
+ATOM 1670 H61 RA 53 85.250 62.140 8.710 1.00 0.00
+ATOM 1671 H62 RA 53 84.440 63.620 9.290 1.00 0.00
+ATOM 1672 N1 RA 53 85.230 63.630 11.550 1.00 0.00
+ATOM 1673 C2 RA 53 85.700 63.570 12.790 1.00 0.00
+ATOM 1674 H2 RA 53 85.540 64.440 13.410 1.00 0.00
+ATOM 1675 N3 RA 53 86.350 62.530 13.290 1.00 0.00
+ATOM 1676 C4 RA 53 86.640 61.540 12.420 1.00 0.00
+ATOM 1677 C3' RA 53 88.850 58.370 15.480 1.00 0.00
+ATOM 1678 H3' RA 53 89.650 57.630 15.530 1.00 0.00
+ATOM 1679 C2' RA 53 88.190 58.380 14.100 1.00 0.00
+ATOM 1680 1H2' RA 53 88.930 58.220 13.310 1.00 0.00
+ATOM 1681 O2' RA 53 87.140 57.470 13.890 1.00 0.00
+ATOM 1682 2HO' RA 53 87.290 56.780 14.540 1.00 0.00
+ATOM 1683 O3' RA 53 87.960 58.190 16.550 1.00 0.00
+ATOM 1684 P RA 54 87.460 56.760 17.100 1.00 0.00
+ATOM 1685 O1P RA 54 88.320 56.460 18.270 1.00 0.00
+ATOM 1686 O2P RA 54 87.400 55.790 15.980 1.00 0.00
+ATOM 1687 O5' RA 54 86.020 56.980 17.780 1.00 0.00
+ATOM 1688 C5' RA 54 84.860 57.450 17.120 1.00 0.00
+ATOM 1689 1H5' RA 54 83.970 57.030 17.590 1.00 0.00
+ATOM 1690 2H5' RA 54 84.810 56.990 16.130 1.00 0.00
+ATOM 1691 C4' RA 54 84.630 58.960 17.150 1.00 0.00
+ATOM 1692 H4' RA 54 85.080 59.430 18.030 1.00 0.00
+ATOM 1693 O4' RA 54 85.260 59.660 16.110 1.00 0.00
+ATOM 1694 C1' RA 54 84.390 60.650 15.600 1.00 0.00
+ATOM 1695 H1' RA 54 84.930 61.590 15.520 1.00 0.00
+ATOM 1696 N9 RA 54 83.910 60.270 14.260 1.00 0.00
+ATOM 1697 C8 RA 54 84.150 59.120 13.550 1.00 0.00
+ATOM 1698 H8 RA 54 84.890 58.400 13.890 1.00 0.00
+ATOM 1699 N7 RA 54 83.370 59.010 12.520 1.00 0.00
+ATOM 1700 C5 RA 54 82.750 60.250 12.390 1.00 0.00
+ATOM 1701 C6 RA 54 81.840 60.870 11.510 1.00 0.00
+ATOM 1702 N6 RA 54 81.230 60.310 10.460 1.00 0.00
+ATOM 1703 H61 RA 54 81.720 59.520 10.070 1.00 0.00
+ATOM 1704 H62 RA 54 80.480 60.830 10.020 1.00 0.00
+ATOM 1705 N1 RA 54 81.330 62.070 11.780 1.00 0.00
+ATOM 1706 C2 RA 54 81.670 62.630 12.940 1.00 0.00
+ATOM 1707 H2 RA 54 81.270 63.620 13.060 1.00 0.00
+ATOM 1708 N3 RA 54 82.440 62.150 13.900 1.00 0.00
+ATOM 1709 C4 RA 54 83.010 60.980 13.510 1.00 0.00
+ATOM 1710 C3' RA 54 83.140 59.300 17.120 1.00 0.00
+ATOM 1711 H3' RA 54 82.690 58.590 16.430 1.00 0.00
+ATOM 1712 C2' RA 54 83.200 60.720 16.550 1.00 0.00
+ATOM 1713 1H2' RA 54 82.230 60.990 16.150 1.00 0.00
+ATOM 1714 O2' RA 54 83.520 61.550 17.650 1.00 0.00
+ATOM 1715 2HO' RA 54 82.930 61.290 18.360 1.00 0.00
+ATOM 1716 O3' RA 54 82.560 59.330 18.400 1.00 0.00
+ATOM 1717 P RC 55 81.300 58.410 18.770 1.00 0.00
+ATOM 1718 O1P RC 55 80.820 58.810 20.110 1.00 0.00
+ATOM 1719 O2P RC 55 81.710 57.020 18.490 1.00 0.00
+ATOM 1720 O5' RC 55 80.120 58.780 17.740 1.00 0.00
+ATOM 1721 C5' RC 55 79.010 59.630 17.980 1.00 0.00
+ATOM 1722 1H5' RC 55 78.520 59.320 18.900 1.00 0.00
+ATOM 1723 2H5' RC 55 78.210 59.550 17.250 1.00 0.00
+ATOM 1724 C4' RC 55 79.540 61.050 17.890 1.00 0.00
+ATOM 1725 H4' RC 55 80.360 61.190 18.590 1.00 0.00
+ATOM 1726 O4' RC 55 79.900 61.420 16.570 1.00 0.00
+ATOM 1727 C1' RC 55 79.420 62.690 16.200 1.00 0.00
+ATOM 1728 H1' RC 55 80.200 63.380 15.870 1.00 0.00
+ATOM 1729 N1 RC 55 78.470 62.580 15.080 1.00 0.00
+ATOM 1730 C6 RC 55 78.150 61.440 14.400 1.00 0.00
+ATOM 1731 H6 RC 55 78.530 60.530 14.830 1.00 0.00
+ATOM 1732 C5 RC 55 77.280 61.420 13.360 1.00 0.00
+ATOM 1733 H5 RC 55 76.910 60.470 13.000 1.00 0.00
+ATOM 1734 C4 RC 55 76.810 62.700 12.920 1.00 0.00
+ATOM 1735 N4 RC 55 75.960 62.900 11.910 1.00 0.00
+ATOM 1736 H41 RC 55 75.460 62.200 11.380 1.00 0.00
+ATOM 1737 H42 RC 55 75.630 63.850 11.780 1.00 0.00
+ATOM 1738 N3 RC 55 77.020 63.830 13.610 1.00 0.00
+ATOM 1739 C2 RC 55 77.830 63.750 14.700 1.00 0.00
+ATOM 1740 O2 RC 55 78.000 64.800 15.300 1.00 0.00
+ATOM 1741 C3' RC 55 78.440 62.000 18.360 1.00 0.00
+ATOM 1742 H3' RC 55 77.490 61.540 18.080 1.00 0.00
+ATOM 1743 C2' RC 55 78.920 63.200 17.550 1.00 0.00
+ATOM 1744 1H2' RC 55 78.090 63.900 17.420 1.00 0.00
+ATOM 1745 O2' RC 55 80.000 63.840 18.190 1.00 0.00
+ATOM 1746 2HO' RC 55 79.940 63.830 19.150 1.00 0.00
+ATOM 1747 O3' RC 55 78.550 62.190 19.750 1.00 0.00
+ATOM 1748 P RU 56 77.280 61.880 20.690 1.00 0.00
+ATOM 1749 O1P RU 56 77.780 61.980 22.080 1.00 0.00
+ATOM 1750 O2P RU 56 76.520 60.690 20.250 1.00 0.00
+ATOM 1751 O5' RU 56 76.390 63.200 20.440 1.00 0.00
+ATOM 1752 C5' RU 56 76.890 64.490 20.740 1.00 0.00
+ATOM 1753 1H5' RU 56 77.960 64.560 20.580 1.00 0.00
+ATOM 1754 2H5' RU 56 76.600 64.730 21.760 1.00 0.00
+ATOM 1755 C4' RU 56 76.100 65.480 19.880 1.00 0.00
+ATOM 1756 H4' RU 56 76.500 66.490 19.920 1.00 0.00
+ATOM 1757 O4' RU 56 76.100 65.110 18.520 1.00 0.00
+ATOM 1758 C1' RU 56 75.030 65.790 17.900 1.00 0.00
+ATOM 1759 H1' RU 56 75.520 66.710 17.590 1.00 0.00
+ATOM 1760 N1 RU 56 74.570 65.110 16.670 1.00 0.00
+ATOM 1761 C6 RU 56 74.840 63.800 16.410 1.00 0.00
+ATOM 1762 H6 RU 56 75.560 63.220 16.970 1.00 0.00
+ATOM 1763 C5 RU 56 74.170 63.100 15.460 1.00 0.00
+ATOM 1764 H5 RU 56 74.500 62.090 15.290 1.00 0.00
+ATOM 1765 C4 RU 56 73.130 63.730 14.690 1.00 0.00
+ATOM 1766 O4 RU 56 72.510 63.190 13.780 1.00 0.00
+ATOM 1767 N3 RU 56 72.840 65.050 15.020 1.00 0.00
+ATOM 1768 H3 RU 56 72.120 65.550 14.530 1.00 0.00
+ATOM 1769 C2 RU 56 73.610 65.770 15.930 1.00 0.00
+ATOM 1770 O2 RU 56 73.330 66.940 16.160 1.00 0.00
+ATOM 1771 C3' RU 56 74.620 65.510 20.250 1.00 0.00
+ATOM 1772 H3' RU 56 74.300 64.470 20.310 1.00 0.00
+ATOM 1773 C2' RU 56 73.990 66.080 18.980 1.00 0.00
+ATOM 1774 1H2' RU 56 73.050 65.570 18.780 1.00 0.00
+ATOM 1775 O2' RU 56 73.890 67.480 19.060 1.00 0.00
+ATOM 1776 2HO' RU 56 73.010 67.720 19.370 1.00 0.00
+ATOM 1777 O3' RU 56 74.310 66.140 21.470 1.00 0.00
+ATOM 1778 P RC 57 72.880 66.060 22.210 1.00 0.00
+ATOM 1779 O1P RC 57 73.050 66.340 23.650 1.00 0.00
+ATOM 1780 O2P RC 57 72.230 64.800 21.790 1.00 0.00
+ATOM 1781 O5' RC 57 72.000 67.230 21.540 1.00 0.00
+ATOM 1782 C5' RC 57 72.190 68.580 21.900 1.00 0.00
+ATOM 1783 1H5' RC 57 73.230 68.890 21.780 1.00 0.00
+ATOM 1784 2H5' RC 57 71.830 68.780 22.910 1.00 0.00
+ATOM 1785 C4' RC 57 71.370 69.430 20.930 1.00 0.00
+ATOM 1786 H4' RC 57 71.800 70.430 21.030 1.00 0.00
+ATOM 1787 O4' RC 57 71.760 69.100 19.620 1.00 0.00
+ATOM 1788 C1' RC 57 70.640 69.210 18.760 1.00 0.00
+ATOM 1789 H1' RC 57 70.840 69.970 18.000 1.00 0.00
+ATOM 1790 N1 RC 57 70.370 67.920 18.100 1.00 0.00
+ATOM 1791 C6 RC 57 70.530 66.730 18.740 1.00 0.00
+ATOM 1792 H6 RC 57 70.740 66.740 19.800 1.00 0.00
+ATOM 1793 C5 RC 57 70.390 65.560 18.090 1.00 0.00
+ATOM 1794 H5 RC 57 70.550 64.620 18.610 1.00 0.00
+ATOM 1795 C4 RC 57 70.050 65.650 16.700 1.00 0.00
+ATOM 1796 N4 RC 57 70.000 64.530 15.970 1.00 0.00
+ATOM 1797 H41 RC 57 70.180 63.630 16.380 1.00 0.00
+ATOM 1798 H42 RC 57 69.740 64.670 15.000 1.00 0.00
+ATOM 1799 N3 RC 57 69.900 66.820 16.070 1.00 0.00
+ATOM 1800 C2 RC 57 70.070 67.990 16.750 1.00 0.00
+ATOM 1801 O2 RC 57 69.820 69.010 16.110 1.00 0.00
+ATOM 1802 C3' RC 57 69.860 69.290 21.080 1.00 0.00
+ATOM 1803 H3' RC 57 69.560 68.240 21.130 1.00 0.00
+ATOM 1804 C2' RC 57 69.530 69.750 19.660 1.00 0.00
+ATOM 1805 1H2' RC 57 68.600 69.250 19.400 1.00 0.00
+ATOM 1806 O2' RC 57 69.380 71.150 19.580 1.00 0.00
+ATOM 1807 2HO' RC 57 69.310 71.530 20.460 1.00 0.00
+ATOM 1808 O3' RC 57 69.400 70.200 22.050 1.00 0.00
+ATOM 1809 P RU 58 67.920 70.050 22.670 1.00 0.00
+ATOM 1810 O1P RU 58 67.760 71.220 23.560 1.00 0.00
+ATOM 1811 O2P RU 58 67.820 68.690 23.240 1.00 0.00
+ATOM 1812 O5' RU 58 66.830 70.180 21.500 1.00 0.00
+ATOM 1813 C5' RU 58 66.380 71.420 21.000 1.00 0.00
+ATOM 1814 1H5' RU 58 67.180 71.950 20.470 1.00 0.00
+ATOM 1815 2H5' RU 58 65.940 71.960 21.830 1.00 0.00
+ATOM 1816 C4' RU 58 65.420 71.300 19.820 1.00 0.00
+ATOM 1817 H4' RU 58 64.980 72.260 19.560 1.00 0.00
+ATOM 1818 O4' RU 58 66.070 70.860 18.650 1.00 0.00
+ATOM 1819 C1' RU 58 65.240 70.040 17.850 1.00 0.00
+ATOM 1820 H1' RU 58 65.240 70.490 16.860 1.00 0.00
+ATOM 1821 N1 RU 58 65.780 68.680 17.670 1.00 0.00
+ATOM 1822 C6 RU 58 66.350 67.970 18.690 1.00 0.00
+ATOM 1823 H6 RU 58 66.560 68.410 19.650 1.00 0.00
+ATOM 1824 C5 RU 58 66.710 66.680 18.550 1.00 0.00
+ATOM 1825 H5 RU 58 67.200 66.200 19.390 1.00 0.00
+ATOM 1826 C4 RU 58 66.500 65.980 17.310 1.00 0.00
+ATOM 1827 O4 RU 58 66.810 64.820 17.070 1.00 0.00
+ATOM 1828 N3 RU 58 65.930 66.760 16.310 1.00 0.00
+ATOM 1829 H3 RU 58 65.560 66.330 15.480 1.00 0.00
+ATOM 1830 C2 RU 58 65.520 68.080 16.450 1.00 0.00
+ATOM 1831 O2 RU 58 64.800 68.550 15.570 1.00 0.00
+ATOM 1832 C3' RU 58 64.220 70.380 20.050 1.00 0.00
+ATOM 1833 H3' RU 58 64.610 69.520 20.600 1.00 0.00
+ATOM 1834 C2' RU 58 63.920 70.010 18.610 1.00 0.00
+ATOM 1835 1H2' RU 58 63.390 69.060 18.610 1.00 0.00
+ATOM 1836 O2' RU 58 63.200 71.000 17.900 1.00 0.00
+ATOM 1837 2HO' RU 58 62.300 71.000 18.240 1.00 0.00
+ATOM 1838 O3' RU 58 63.230 71.200 20.640 1.00 0.00
+ATOM 1839 P RU 59 61.850 70.600 21.210 1.00 0.00
+ATOM 1840 O1P RU 59 61.150 71.740 21.840 1.00 0.00
+ATOM 1841 O2P RU 59 62.250 69.400 21.980 1.00 0.00
+ATOM 1842 O5' RU 59 60.990 70.200 19.900 1.00 0.00
+ATOM 1843 C5' RU 59 60.210 70.990 19.040 1.00 0.00
+ATOM 1844 1H5' RU 59 60.820 71.780 18.610 1.00 0.00
+ATOM 1845 2H5' RU 59 59.420 71.480 19.600 1.00 0.00
+ATOM 1846 C4' RU 59 59.680 70.150 17.880 1.00 0.00
+ATOM 1847 H4' RU 59 59.090 70.830 17.250 1.00 0.00
+ATOM 1848 O4' RU 59 60.710 69.420 17.260 1.00 0.00
+ATOM 1849 C1' RU 59 60.160 68.300 16.610 1.00 0.00
+ATOM 1850 H1' RU 59 60.140 68.270 15.520 1.00 0.00
+ATOM 1851 N1 RU 59 61.000 67.140 16.960 1.00 0.00
+ATOM 1852 C6 RU 59 61.800 67.060 18.060 1.00 0.00
+ATOM 1853 H6 RU 59 61.640 67.850 18.780 1.00 0.00
+ATOM 1854 C5 RU 59 62.710 66.100 18.330 1.00 0.00
+ATOM 1855 H5 RU 59 63.340 65.970 19.200 1.00 0.00
+ATOM 1856 C4 RU 59 62.830 65.040 17.360 1.00 0.00
+ATOM 1857 O4 RU 59 63.480 64.000 17.460 1.00 0.00
+ATOM 1858 N3 RU 59 62.040 65.110 16.220 1.00 0.00
+ATOM 1859 H3 RU 59 62.030 64.390 15.510 1.00 0.00
+ATOM 1860 C2 RU 59 61.050 66.070 16.070 1.00 0.00
+ATOM 1861 O2 RU 59 60.220 65.950 15.170 1.00 0.00
+ATOM 1862 C3' RU 59 58.770 69.030 18.360 1.00 0.00
+ATOM 1863 H3' RU 59 59.270 68.520 19.190 1.00 0.00
+ATOM 1864 C2' RU 59 58.730 68.140 17.120 1.00 0.00
+ATOM 1865 1H2' RU 59 58.500 67.140 17.490 1.00 0.00
+ATOM 1866 O2' RU 59 57.810 68.530 16.130 1.00 0.00
+ATOM 1867 2HO' RU 59 57.010 68.750 16.610 1.00 0.00
+ATOM 1868 O3' RU 59 57.510 69.540 18.720 1.00 0.00
+ATOM 1869 P RG 60 56.570 68.670 19.710 1.00 0.00
+ATOM 1870 O1P RG 60 55.250 69.310 19.930 1.00 0.00
+ATOM 1871 O2P RG 60 57.270 68.150 20.910 1.00 0.00
+ATOM 1872 O5' RG 60 56.300 67.370 18.800 1.00 0.00
+ATOM 1873 C5' RG 60 55.340 67.160 17.790 1.00 0.00
+ATOM 1874 1H5' RG 60 55.510 67.830 16.950 1.00 0.00
+ATOM 1875 2H5' RG 60 54.370 67.420 18.200 1.00 0.00
+ATOM 1876 C4' RG 60 55.280 65.700 17.360 1.00 0.00
+ATOM 1877 H4' RG 60 54.470 65.620 16.640 1.00 0.00
+ATOM 1878 O4' RG 60 56.390 65.260 16.610 1.00 0.00
+ATOM 1879 C1' RG 60 56.560 63.890 16.880 1.00 0.00
+ATOM 1880 H1' RG 60 56.510 63.400 15.910 1.00 0.00
+ATOM 1881 N9 RG 60 57.920 63.530 17.360 1.00 0.00
+ATOM 1882 C8 RG 60 58.650 64.170 18.330 1.00 0.00
+ATOM 1883 H8 RG 60 58.460 65.160 18.720 1.00 0.00
+ATOM 1884 N7 RG 60 59.710 63.510 18.710 1.00 0.00
+ATOM 1885 C5 RG 60 59.730 62.420 17.850 1.00 0.00
+ATOM 1886 C6 RG 60 60.600 61.310 17.800 1.00 0.00
+ATOM 1887 O6 RG 60 61.540 61.040 18.550 1.00 0.00
+ATOM 1888 N1 RG 60 60.300 60.360 16.830 1.00 0.00
+ATOM 1889 H1 RG 60 60.710 59.440 16.780 1.00 0.00
+ATOM 1890 C2 RG 60 59.290 60.590 15.920 1.00 0.00
+ATOM 1891 N2 RG 60 59.020 59.670 14.980 1.00 0.00
+ATOM 1892 H21 RG 60 59.590 58.840 14.930 1.00 0.00
+ATOM 1893 H22 RG 60 58.370 59.900 14.240 1.00 0.00
+ATOM 1894 N3 RG 60 58.400 61.590 15.970 1.00 0.00
+ATOM 1895 C4 RG 60 58.690 62.470 16.960 1.00 0.00
+ATOM 1896 C3' RG 60 54.930 64.670 18.430 1.00 0.00
+ATOM 1897 H3' RG 60 55.610 64.760 19.280 1.00 0.00
+ATOM 1898 C2' RG 60 55.420 63.390 17.770 1.00 0.00
+ATOM 1899 1H2' RG 60 55.770 62.680 18.520 1.00 0.00
+ATOM 1900 O2' RG 60 54.510 62.680 16.960 1.00 0.00
+ATOM 1901 2HO' RG 60 53.680 62.450 17.390 1.00 0.00
+ATOM 1902 O3' RG 60 53.600 64.770 18.880 1.00 0.00
+ATOM 1903 P RA 61 53.000 63.740 19.960 1.00 0.00
+ATOM 1904 O1P RA 61 51.620 64.120 20.330 1.00 0.00
+ATOM 1905 O2P RA 61 53.910 63.590 21.120 1.00 0.00
+ATOM 1906 O5' RA 61 52.970 62.280 19.280 1.00 0.00
+ATOM 1907 C5' RA 61 52.200 61.160 19.650 1.00 0.00
+ATOM 1908 1H5' RA 61 51.110 61.220 19.590 1.00 0.00
+ATOM 1909 2H5' RA 61 52.440 61.000 20.700 1.00 0.00
+ATOM 1910 C4' RA 61 52.650 60.030 18.720 1.00 0.00
+ATOM 1911 H4' RA 61 52.210 60.220 17.750 1.00 0.00
+ATOM 1912 O4' RA 61 54.050 59.860 18.730 1.00 0.00
+ATOM 1913 C1' RA 61 54.300 58.560 19.230 1.00 0.00
+ATOM 1914 H1' RA 61 55.120 58.190 18.620 1.00 0.00
+ATOM 1915 N9 RA 61 54.810 58.530 20.620 1.00 0.00
+ATOM 1916 C8 RA 61 54.870 59.520 21.560 1.00 0.00
+ATOM 1917 H8 RA 61 54.530 60.530 21.390 1.00 0.00
+ATOM 1918 N7 RA 61 55.380 59.120 22.700 1.00 0.00
+ATOM 1919 C5 RA 61 55.680 57.780 22.460 1.00 0.00
+ATOM 1920 C6 RA 61 56.200 56.700 23.190 1.00 0.00
+ATOM 1921 N6 RA 61 56.690 56.810 24.430 1.00 0.00
+ATOM 1922 H61 RA 61 56.900 57.730 24.780 1.00 0.00
+ATOM 1923 H62 RA 61 57.200 56.040 24.840 1.00 0.00
+ATOM 1924 N1 RA 61 56.330 55.460 22.680 1.00 0.00
+ATOM 1925 C2 RA 61 55.960 55.270 21.430 1.00 0.00
+ATOM 1926 H2 RA 61 56.020 54.290 20.980 1.00 0.00
+ATOM 1927 N3 RA 61 55.430 56.170 20.620 1.00 0.00
+ATOM 1928 C4 RA 61 55.280 57.380 21.210 1.00 0.00
+ATOM 1929 C3' RA 61 51.960 58.790 19.290 1.00 0.00
+ATOM 1930 H3' RA 61 51.820 58.980 20.360 1.00 0.00
+ATOM 1931 C2' RA 61 53.030 57.730 19.070 1.00 0.00
+ATOM 1932 1H2' RA 61 52.940 56.990 19.860 1.00 0.00
+ATOM 1933 O2' RA 61 53.100 57.240 17.740 1.00 0.00
+ATOM 1934 2HO' RA 61 53.870 56.690 17.620 1.00 0.00
+ATOM 1935 O3' RA 61 50.710 58.610 18.670 1.00 0.00
+ATOM 1936 P RU 62 49.560 57.690 19.320 1.00 0.00
+ATOM 1937 O1P RU 62 48.590 57.420 18.230 1.00 0.00
+ATOM 1938 O2P RU 62 49.140 58.450 20.510 1.00 0.00
+ATOM 1939 O5' RU 62 50.210 56.320 19.860 1.00 0.00
+ATOM 1940 C5' RU 62 50.540 55.340 18.900 1.00 0.00
+ATOM 1941 1H5' RU 62 51.220 55.860 18.220 1.00 0.00
+ATOM 1942 2H5' RU 62 49.650 55.020 18.350 1.00 0.00
+ATOM 1943 C4' RU 62 51.210 54.070 19.400 1.00 0.00
+ATOM 1944 H4' RU 62 51.370 53.470 18.510 1.00 0.00
+ATOM 1945 O4' RU 62 52.460 54.400 19.970 1.00 0.00
+ATOM 1946 C1' RU 62 52.840 53.420 20.910 1.00 0.00
+ATOM 1947 H1' RU 62 53.740 52.930 20.550 1.00 0.00
+ATOM 1948 N1 RU 62 52.960 53.920 22.290 1.00 0.00
+ATOM 1949 C6 RU 62 52.640 55.200 22.660 1.00 0.00
+ATOM 1950 H6 RU 62 52.180 55.890 21.980 1.00 0.00
+ATOM 1951 C5 RU 62 52.950 55.680 23.890 1.00 0.00
+ATOM 1952 H5 RU 62 52.850 56.720 24.160 1.00 0.00
+ATOM 1953 C4 RU 62 53.610 54.780 24.800 1.00 0.00
+ATOM 1954 O4 RU 62 53.920 55.110 25.950 1.00 0.00
+ATOM 1955 N3 RU 62 53.880 53.490 24.370 1.00 0.00
+ATOM 1956 H3 RU 62 54.350 52.870 25.020 1.00 0.00
+ATOM 1957 C2 RU 62 53.650 53.020 23.080 1.00 0.00
+ATOM 1958 O2 RU 62 54.070 51.910 22.770 1.00 0.00
+ATOM 1959 C3' RU 62 50.500 53.240 20.470 1.00 0.00
+ATOM 1960 H3' RU 62 50.180 53.880 21.290 1.00 0.00
+ATOM 1961 C2' RU 62 51.720 52.390 20.800 1.00 0.00
+ATOM 1962 1H2' RU 62 51.520 51.910 21.760 1.00 0.00
+ATOM 1963 O2' RU 62 52.050 51.430 19.820 1.00 0.00
+ATOM 1964 2HO' RU 62 51.200 51.140 19.480 1.00 0.00
+ATOM 1965 O3' RU 62 49.400 52.550 19.920 1.00 0.00
+ATOM 1966 P RU 63 48.380 51.830 20.940 1.00 0.00
+ATOM 1967 O1P RU 63 47.580 50.880 20.130 1.00 0.00
+ATOM 1968 O2P RU 63 47.660 52.890 21.670 1.00 0.00
+ATOM 1969 O5' RU 63 49.240 50.990 22.010 1.00 0.00
+ATOM 1970 C5' RU 63 49.770 49.740 21.620 1.00 0.00
+ATOM 1971 1H5' RU 63 50.370 49.830 20.710 1.00 0.00
+ATOM 1972 2H5' RU 63 48.910 49.140 21.330 1.00 0.00
+ATOM 1973 C4' RU 63 50.570 49.160 22.780 1.00 0.00
+ATOM 1974 H4' RU 63 51.050 48.240 22.440 1.00 0.00
+ATOM 1975 O4' RU 63 51.560 50.020 23.320 1.00 0.00
+ATOM 1976 C1' RU 63 51.670 49.850 24.710 1.00 0.00
+ATOM 1977 H1' RU 63 52.680 49.520 24.970 1.00 0.00
+ATOM 1978 N1 RU 63 51.380 51.120 25.400 1.00 0.00
+ATOM 1979 C6 RU 63 50.690 52.190 24.910 1.00 0.00
+ATOM 1980 H6 RU 63 50.290 52.150 23.910 1.00 0.00
+ATOM 1981 C5 RU 63 50.440 53.230 25.730 1.00 0.00
+ATOM 1982 H5 RU 63 49.800 54.060 25.460 1.00 0.00
+ATOM 1983 C4 RU 63 50.940 53.320 27.080 1.00 0.00
+ATOM 1984 O4 RU 63 50.780 54.260 27.850 1.00 0.00
+ATOM 1985 N3 RU 63 51.650 52.200 27.480 1.00 0.00
+ATOM 1986 H3 RU 63 51.950 52.290 28.440 1.00 0.00
+ATOM 1987 C2 RU 63 51.810 51.050 26.710 1.00 0.00
+ATOM 1988 O2 RU 63 52.230 50.050 27.290 1.00 0.00
+ATOM 1989 C3' RU 63 49.600 48.850 23.920 1.00 0.00
+ATOM 1990 H3' RU 63 49.030 49.750 24.150 1.00 0.00
+ATOM 1991 C2' RU 63 50.680 48.720 24.980 1.00 0.00
+ATOM 1992 1H2' RU 63 50.270 48.760 25.990 1.00 0.00
+ATOM 1993 O2' RU 63 51.250 47.440 24.790 1.00 0.00
+ATOM 1994 2HO' RU 63 51.420 47.050 25.650 1.00 0.00
+ATOM 1995 O3' RU 63 48.820 47.690 23.750 1.00 0.00
+ATOM 1996 P RA 64 47.390 47.620 24.490 1.00 0.00
+ATOM 1997 O1P RA 64 46.750 46.370 24.020 1.00 0.00
+ATOM 1998 O2P RA 64 46.670 48.900 24.360 1.00 0.00
+ATOM 1999 O5' RA 64 47.710 47.440 26.060 1.00 0.00
+ATOM 2000 C5' RA 64 48.330 46.250 26.500 1.00 0.00
+ATOM 2001 1H5' RA 64 49.120 46.020 25.790 1.00 0.00
+ATOM 2002 2H5' RA 64 47.610 45.430 26.500 1.00 0.00
+ATOM 2003 C4' RA 64 48.900 46.390 27.910 1.00 0.00
+ATOM 2004 H4' RA 64 49.310 45.400 28.090 1.00 0.00
+ATOM 2005 O4' RA 64 49.870 47.410 28.010 1.00 0.00
+ATOM 2006 C1' RA 64 50.000 47.840 29.350 1.00 0.00
+ATOM 2007 H1' RA 64 50.960 47.590 29.810 1.00 0.00
+ATOM 2008 N9 RA 64 49.700 49.290 29.360 1.00 0.00
+ATOM 2009 C8 RA 64 49.160 50.040 28.350 1.00 0.00
+ATOM 2010 H8 RA 64 48.940 49.640 27.370 1.00 0.00
+ATOM 2011 N7 RA 64 48.800 51.250 28.680 1.00 0.00
+ATOM 2012 C5 RA 64 49.200 51.330 30.010 1.00 0.00
+ATOM 2013 C6 RA 64 49.220 52.370 30.950 1.00 0.00
+ATOM 2014 N6 RA 64 48.850 53.640 30.710 1.00 0.00
+ATOM 2015 H61 RA 64 48.580 53.900 29.770 1.00 0.00
+ATOM 2016 H62 RA 64 48.910 54.360 31.420 1.00 0.00
+ATOM 2017 N1 RA 64 49.670 52.160 32.190 1.00 0.00
+ATOM 2018 C2 RA 64 50.050 50.930 32.510 1.00 0.00
+ATOM 2019 H2 RA 64 50.530 50.860 33.470 1.00 0.00
+ATOM 2020 N3 RA 64 50.130 49.880 31.710 1.00 0.00
+ATOM 2021 C4 RA 64 49.740 50.140 30.440 1.00 0.00
+ATOM 2022 C3' RA 64 47.940 46.800 29.030 1.00 0.00
+ATOM 2023 H3' RA 64 47.440 47.730 28.770 1.00 0.00
+ATOM 2024 C2' RA 64 48.930 47.120 30.150 1.00 0.00
+ATOM 2025 1H2' RA 64 48.490 47.670 30.980 1.00 0.00
+ATOM 2026 O2' RA 64 49.400 45.860 30.590 1.00 0.00
+ATOM 2027 2HO' RA 64 50.320 45.990 30.840 1.00 0.00
+ATOM 2028 O3' RA 64 46.900 45.870 29.240 1.00 0.00
+ATOM 2029 P RU 65 45.650 46.230 30.180 1.00 0.00
+ATOM 2030 O1P RU 65 44.960 44.970 30.530 1.00 0.00
+ATOM 2031 O2P RU 65 44.930 47.370 29.560 1.00 0.00
+ATOM 2032 O5' RU 65 46.160 46.830 31.590 1.00 0.00
+ATOM 2033 C5' RU 65 46.790 46.110 32.620 1.00 0.00
+ATOM 2034 1H5' RU 65 47.680 45.700 32.150 1.00 0.00
+ATOM 2035 2H5' RU 65 46.160 45.280 32.930 1.00 0.00
+ATOM 2036 C4' RU 65 47.040 47.030 33.810 1.00 0.00
+ATOM 2037 H4' RU 65 47.520 46.440 34.590 1.00 0.00
+ATOM 2038 O4' RU 65 47.970 48.060 33.560 1.00 0.00
+ATOM 2039 C1' RU 65 47.530 49.100 34.400 1.00 0.00
+ATOM 2040 H1' RU 65 48.260 49.360 35.170 1.00 0.00
+ATOM 2041 N1 RU 65 47.080 50.310 33.680 1.00 0.00
+ATOM 2042 C6 RU 65 46.540 50.180 32.440 1.00 0.00
+ATOM 2043 H6 RU 65 46.660 49.230 31.930 1.00 0.00
+ATOM 2044 C5 RU 65 46.060 51.260 31.790 1.00 0.00
+ATOM 2045 H5 RU 65 45.830 51.160 30.740 1.00 0.00
+ATOM 2046 C4 RU 65 46.050 52.570 32.400 1.00 0.00
+ATOM 2047 O4 RU 65 45.730 53.660 31.930 1.00 0.00
+ATOM 2048 N3 RU 65 46.570 52.600 33.680 1.00 0.00
+ATOM 2049 H3 RU 65 46.420 53.430 34.250 1.00 0.00
+ATOM 2050 C2 RU 65 47.090 51.510 34.370 1.00 0.00
+ATOM 2051 O2 RU 65 47.610 51.630 35.470 1.00 0.00
+ATOM 2052 C3' RU 65 45.710 47.610 34.290 1.00 0.00
+ATOM 2053 H3' RU 65 45.150 48.030 33.450 1.00 0.00
+ATOM 2054 C2' RU 65 46.280 48.700 35.190 1.00 0.00
+ATOM 2055 1H2' RU 65 45.530 49.470 35.310 1.00 0.00
+ATOM 2056 O2' RU 65 46.750 48.270 36.450 1.00 0.00
+ATOM 2057 2HO' RU 65 45.980 48.300 37.020 1.00 0.00
+ATOM 2058 O3' RU 65 44.890 46.640 34.910 1.00 0.00
+ATOM 2059 P RG 66 43.360 47.020 35.240 1.00 0.00
+ATOM 2060 O1P RG 66 42.640 45.850 35.780 1.00 0.00
+ATOM 2061 O2P RG 66 42.880 47.790 34.070 1.00 0.00
+ATOM 2062 O5' RG 66 43.680 48.000 36.480 1.00 0.00
+ATOM 2063 C5' RG 66 43.860 47.420 37.750 1.00 0.00
+ATOM 2064 1H5' RG 66 44.550 46.580 37.660 1.00 0.00
+ATOM 2065 2H5' RG 66 42.980 46.870 38.100 1.00 0.00
+ATOM 2066 C4' RG 66 44.220 48.500 38.760 1.00 0.00
+ATOM 2067 H4' RG 66 44.780 48.030 39.570 1.00 0.00
+ATOM 2068 O4' RG 66 45.080 49.510 38.290 1.00 0.00
+ATOM 2069 C1' RG 66 44.760 50.780 38.820 1.00 0.00
+ATOM 2070 H1' RG 66 45.640 51.220 39.290 1.00 0.00
+ATOM 2071 N9 RG 66 44.130 51.710 37.870 1.00 0.00
+ATOM 2072 C8 RG 66 43.590 51.420 36.640 1.00 0.00
+ATOM 2073 H8 RG 66 43.570 50.420 36.250 1.00 0.00
+ATOM 2074 N7 RG 66 43.110 52.420 35.950 1.00 0.00
+ATOM 2075 C5 RG 66 43.290 53.470 36.850 1.00 0.00
+ATOM 2076 C6 RG 66 43.110 54.860 36.660 1.00 0.00
+ATOM 2077 O6 RG 66 42.570 55.410 35.700 1.00 0.00
+ATOM 2078 N1 RG 66 43.450 55.610 37.780 1.00 0.00
+ATOM 2079 H1 RG 66 43.450 56.620 37.760 1.00 0.00
+ATOM 2080 C2 RG 66 43.830 55.050 38.990 1.00 0.00
+ATOM 2081 N2 RG 66 43.900 55.890 40.030 1.00 0.00
+ATOM 2082 H21 RG 66 43.490 56.800 39.880 1.00 0.00
+ATOM 2083 H22 RG 66 43.860 55.460 40.940 1.00 0.00
+ATOM 2084 N3 RG 66 44.170 53.760 39.130 1.00 0.00
+ATOM 2085 C4 RG 66 43.820 53.040 38.040 1.00 0.00
+ATOM 2086 C3' RG 66 42.990 49.220 39.290 1.00 0.00
+ATOM 2087 H3' RG 66 42.210 49.450 38.560 1.00 0.00
+ATOM 2088 C2' RG 66 43.710 50.440 39.870 1.00 0.00
+ATOM 2089 1H2' RG 66 42.990 51.240 40.010 1.00 0.00
+ATOM 2090 O2' RG 66 44.420 50.020 41.010 1.00 0.00
+ATOM 2091 2HO' RG 66 44.710 50.850 41.400 1.00 0.00
+ATOM 2092 O3' RG 66 42.490 48.340 40.270 1.00 0.00
+ATOM 2093 P RA 67 40.970 48.390 40.780 1.00 0.00
+ATOM 2094 O1P RA 67 40.840 47.650 42.060 1.00 0.00
+ATOM 2095 O2P RA 67 40.080 48.000 39.660 1.00 0.00
+ATOM 2096 O5' RA 67 40.680 49.940 41.120 1.00 0.00
+ATOM 2097 C5' RA 67 41.060 50.430 42.390 1.00 0.00
+ATOM 2098 1H5' RA 67 42.130 50.230 42.490 1.00 0.00
+ATOM 2099 2H5' RA 67 40.550 49.910 43.200 1.00 0.00
+ATOM 2100 C4' RA 67 40.710 51.910 42.520 1.00 0.00
+ATOM 2101 H4' RA 67 41.030 52.140 43.540 1.00 0.00
+ATOM 2102 O4' RA 67 41.460 52.680 41.600 1.00 0.00
+ATOM 2103 C1' RA 67 40.760 53.880 41.390 1.00 0.00
+ATOM 2104 H1' RA 67 41.370 54.690 41.790 1.00 0.00
+ATOM 2105 N9 RA 67 40.640 54.150 39.940 1.00 0.00
+ATOM 2106 C8 RA 67 40.560 53.190 38.960 1.00 0.00
+ATOM 2107 H8 RA 67 40.680 52.150 39.190 1.00 0.00
+ATOM 2108 N7 RA 67 40.330 53.680 37.770 1.00 0.00
+ATOM 2109 C5 RA 67 40.080 55.020 38.050 1.00 0.00
+ATOM 2110 C6 RA 67 39.600 56.090 37.280 1.00 0.00
+ATOM 2111 N6 RA 67 39.310 56.050 35.970 1.00 0.00
+ATOM 2112 H61 RA 67 39.420 55.230 35.400 1.00 0.00
+ATOM 2113 H62 RA 67 39.070 56.890 35.460 1.00 0.00
+ATOM 2114 N1 RA 67 39.430 57.300 37.830 1.00 0.00
+ATOM 2115 C2 RA 67 39.710 57.490 39.110 1.00 0.00
+ATOM 2116 H2 RA 67 39.560 58.490 39.500 1.00 0.00
+ATOM 2117 N3 RA 67 40.190 56.570 39.930 1.00 0.00
+ATOM 2118 C4 RA 67 40.300 55.350 39.360 1.00 0.00
+ATOM 2119 C3' RA 67 39.260 52.340 42.340 1.00 0.00
+ATOM 2120 H3' RA 67 38.920 51.730 41.500 1.00 0.00
+ATOM 2121 C2' RA 67 39.360 53.820 42.000 1.00 0.00
+ATOM 2122 1H2' RA 67 38.560 54.180 41.350 1.00 0.00
+ATOM 2123 O2' RA 67 39.330 54.660 43.130 1.00 0.00
+ATOM 2124 2HO' RA 67 38.530 55.180 43.140 1.00 0.00
+ATOM 2125 O3' RA 67 38.480 51.960 43.450 1.00 0.00
+ATOM 2126 P RA 68 36.880 51.950 43.270 1.00 0.00
+ATOM 2127 O1P RA 68 36.280 51.530 44.550 1.00 0.00
+ATOM 2128 O2P RA 68 36.530 51.230 42.020 1.00 0.00
+ATOM 2129 O5' RA 68 36.330 53.450 43.080 1.00 0.00
+ATOM 2130 C5' RA 68 36.060 54.180 44.260 1.00 0.00
+ATOM 2131 1H5' RA 68 36.970 54.070 44.850 1.00 0.00
+ATOM 2132 2H5' RA 68 35.200 53.760 44.770 1.00 0.00
+ATOM 2133 C4' RA 68 35.890 55.660 43.900 1.00 0.00
+ATOM 2134 H4' RA 68 35.940 56.240 44.820 1.00 0.00
+ATOM 2135 O4' RA 68 36.790 56.150 42.940 1.00 0.00
+ATOM 2136 C1' RA 68 36.120 57.050 42.090 1.00 0.00
+ATOM 2137 H1' RA 68 36.600 58.020 42.270 1.00 0.00
+ATOM 2138 N9 RA 68 36.090 56.680 40.670 1.00 0.00
+ATOM 2139 C8 RA 68 36.410 55.490 40.070 1.00 0.00
+ATOM 2140 H8 RA 68 36.450 54.570 40.620 1.00 0.00
+ATOM 2141 N7 RA 68 36.380 55.430 38.760 1.00 0.00
+ATOM 2142 C5 RA 68 36.080 56.760 38.480 1.00 0.00
+ATOM 2143 C6 RA 68 36.020 57.480 37.270 1.00 0.00
+ATOM 2144 N6 RA 68 36.270 56.960 36.060 1.00 0.00
+ATOM 2145 H61 RA 68 36.600 56.010 35.940 1.00 0.00
+ATOM 2146 H62 RA 68 36.150 57.620 35.310 1.00 0.00
+ATOM 2147 N1 RA 68 35.660 58.770 37.250 1.00 0.00
+ATOM 2148 C2 RA 68 35.380 59.370 38.390 1.00 0.00
+ATOM 2149 H2 RA 68 35.220 60.430 38.300 1.00 0.00
+ATOM 2150 N3 RA 68 35.460 58.810 39.590 1.00 0.00
+ATOM 2151 C4 RA 68 35.820 57.500 39.600 1.00 0.00
+ATOM 2152 C3' RA 68 34.480 55.830 43.360 1.00 0.00
+ATOM 2153 H3' RA 68 34.170 55.100 42.610 1.00 0.00
+ATOM 2154 C2' RA 68 34.690 57.150 42.610 1.00 0.00
+ATOM 2155 1H2' RA 68 33.980 57.230 41.790 1.00 0.00
+ATOM 2156 O2' RA 68 34.540 58.260 43.460 1.00 0.00
+ATOM 2157 2HO' RA 68 34.050 58.940 42.980 1.00 0.00
+ATOM 2158 O3' RA 68 33.520 55.940 44.390 1.00 0.00
+ATOM 2159 P RG 69 32.100 55.220 44.150 1.00 0.00
+ATOM 2160 O1P RG 69 31.430 55.160 45.470 1.00 0.00
+ATOM 2161 O2P RG 69 32.240 54.000 43.320 1.00 0.00
+ATOM 2162 O5' RG 69 31.380 56.320 43.230 1.00 0.00
+ATOM 2163 C5' RG 69 30.990 57.570 43.760 1.00 0.00
+ATOM 2164 1H5' RG 69 31.790 57.860 44.440 1.00 0.00
+ATOM 2165 2H5' RG 69 30.070 57.620 44.340 1.00 0.00
+ATOM 2166 C4' RG 69 30.840 58.660 42.700 1.00 0.00
+ATOM 2167 H4' RG 69 30.770 59.580 43.280 1.00 0.00
+ATOM 2168 O4' RG 69 31.960 58.770 41.850 1.00 0.00
+ATOM 2169 C1' RG 69 31.660 59.300 40.580 1.00 0.00
+ATOM 2170 H1' RG 69 32.180 60.250 40.440 1.00 0.00
+ATOM 2171 N9 RG 69 32.020 58.340 39.520 1.00 0.00
+ATOM 2172 C8 RG 69 32.360 57.010 39.590 1.00 0.00
+ATOM 2173 H8 RG 69 32.520 56.490 40.520 1.00 0.00
+ATOM 2174 N7 RG 69 32.590 56.470 38.420 1.00 0.00
+ATOM 2175 C5 RG 69 32.320 57.490 37.520 1.00 0.00
+ATOM 2176 C6 RG 69 32.350 57.490 36.100 1.00 0.00
+ATOM 2177 O6 RG 69 32.640 56.550 35.360 1.00 0.00
+ATOM 2178 N1 RG 69 32.000 58.710 35.540 1.00 0.00
+ATOM 2179 H1 RG 69 31.590 58.780 34.620 1.00 0.00
+ATOM 2180 C2 RG 69 31.780 59.830 36.320 1.00 0.00
+ATOM 2181 N2 RG 69 31.310 60.950 35.750 1.00 0.00
+ATOM 2182 H21 RG 69 31.080 60.940 34.770 1.00 0.00
+ATOM 2183 H22 RG 69 31.230 61.790 36.300 1.00 0.00
+ATOM 2184 N3 RG 69 31.700 59.840 37.650 1.00 0.00
+ATOM 2185 C4 RG 69 32.060 58.650 38.190 1.00 0.00
+ATOM 2186 C3' RG 69 29.660 58.650 41.740 1.00 0.00
+ATOM 2187 H3' RG 69 29.480 57.680 41.270 1.00 0.00
+ATOM 2188 C2' RG 69 30.170 59.630 40.690 1.00 0.00
+ATOM 2189 1H2' RG 69 29.780 59.540 39.680 1.00 0.00
+ATOM 2190 O2' RG 69 30.010 60.980 41.060 1.00 0.00
+ATOM 2191 2HO' RG 69 29.140 61.060 41.450 1.00 0.00
+ATOM 2192 O3' RG 69 28.530 59.280 42.300 1.00 0.00
+ATOM 2193 P RU 70 27.070 58.620 42.180 1.00 0.00
+ATOM 2194 O1P RU 70 26.170 59.570 42.880 1.00 0.00
+ATOM 2195 O2P RU 70 27.020 57.210 42.610 1.00 0.00
+ATOM 2196 O5' RU 70 26.710 58.600 40.610 1.00 0.00
+ATOM 2197 C5' RU 70 26.600 59.760 39.810 1.00 0.00
+ATOM 2198 1H5' RU 70 27.160 60.640 40.130 1.00 0.00
+ATOM 2199 2H5' RU 70 25.550 60.010 39.930 1.00 0.00
+ATOM 2200 C4' RU 70 26.850 59.590 38.310 1.00 0.00
+ATOM 2201 H4' RU 70 26.890 60.550 37.800 1.00 0.00
+ATOM 2202 O4' RU 70 28.100 58.970 38.150 1.00 0.00
+ATOM 2203 C1' RU 70 28.140 58.210 36.960 1.00 0.00
+ATOM 2204 H1' RU 70 28.730 58.740 36.210 1.00 0.00
+ATOM 2205 N1 RU 70 28.760 56.900 37.240 1.00 0.00
+ATOM 2206 C6 RU 70 28.790 56.420 38.520 1.00 0.00
+ATOM 2207 H6 RU 70 28.370 56.980 39.340 1.00 0.00
+ATOM 2208 C5 RU 70 29.340 55.210 38.760 1.00 0.00
+ATOM 2209 H5 RU 70 29.360 54.850 39.780 1.00 0.00
+ATOM 2210 C4 RU 70 29.810 54.350 37.700 1.00 0.00
+ATOM 2211 O4 RU 70 30.390 53.290 37.910 1.00 0.00
+ATOM 2212 N3 RU 70 29.690 54.910 36.430 1.00 0.00
+ATOM 2213 H3 RU 70 30.080 54.330 35.700 1.00 0.00
+ATOM 2214 C2 RU 70 29.260 56.200 36.150 1.00 0.00
+ATOM 2215 O2 RU 70 29.250 56.620 35.000 1.00 0.00
+ATOM 2216 C3' RU 70 25.860 58.670 37.600 1.00 0.00
+ATOM 2217 H3' RU 70 25.620 57.900 38.330 1.00 0.00
+ATOM 2218 C2' RU 70 26.700 58.100 36.460 1.00 0.00
+ATOM 2219 1H2' RU 70 26.360 57.070 36.400 1.00 0.00
+ATOM 2220 O2' RU 70 26.660 58.790 35.230 1.00 0.00
+ATOM 2221 2HO' RU 70 25.770 59.120 35.110 1.00 0.00
+ATOM 2222 O3' RU 70 24.610 59.220 37.260 1.00 0.00
+ATOM 2223 P RG3 71 23.370 58.370 36.680 1.00 0.00
+ATOM 2224 O1P RG3 71 22.040 58.940 37.000 1.00 0.00
+ATOM 2225 O2P RG3 71 23.470 56.940 37.050 1.00 0.00
+ATOM 2226 O5' RG3 71 23.610 58.510 35.090 1.00 0.00
+ATOM 2227 C5' RG3 71 23.480 59.760 34.460 1.00 0.00
+ATOM 2228 1H5' RG3 71 24.120 60.500 34.950 1.00 0.00
+ATOM 2229 2H5' RG3 71 22.450 60.030 34.670 1.00 0.00
+ATOM 2230 C4' RG3 71 23.610 59.790 32.940 1.00 0.00
+ATOM 2231 H4' RG3 71 23.540 60.820 32.600 1.00 0.00
+ATOM 2232 O4' RG3 71 24.810 59.200 32.510 1.00 0.00
+ATOM 2233 C1' RG3 71 24.460 58.340 31.450 1.00 0.00
+ATOM 2234 H1' RG3 71 25.040 58.610 30.570 1.00 0.00
+ATOM 2235 N9 RG3 71 24.880 56.960 31.760 1.00 0.00
+ATOM 2236 C8 RG3 71 25.100 56.440 33.010 1.00 0.00
+ATOM 2237 H8 RG3 71 24.990 57.050 33.900 1.00 0.00
+ATOM 2238 N7 RG3 71 25.540 55.210 33.040 1.00 0.00
+ATOM 2239 C5 RG3 71 25.590 54.900 31.680 1.00 0.00
+ATOM 2240 C6 RG3 71 26.040 53.720 31.040 1.00 0.00
+ATOM 2241 O6 RG3 71 26.570 52.700 31.470 1.00 0.00
+ATOM 2242 N1 RG3 71 25.930 53.750 29.650 1.00 0.00
+ATOM 2243 H1 RG3 71 26.400 52.980 29.200 1.00 0.00
+ATOM 2244 C2 RG3 71 25.530 54.870 28.940 1.00 0.00
+ATOM 2245 N2 RG3 71 25.660 54.690 27.620 1.00 0.00
+ATOM 2246 H21 RG3 71 25.960 53.830 27.190 1.00 0.00
+ATOM 2247 H22 RG3 71 25.340 55.460 27.050 1.00 0.00
+ATOM 2248 N3 RG3 71 25.180 56.010 29.540 1.00 0.00
+ATOM 2249 C4 RG3 71 25.160 55.930 30.890 1.00 0.00
+ATOM 2250 C3' RG3 71 22.440 58.930 32.460 1.00 0.00
+ATOM 2251 H3' RG3 71 22.230 58.090 33.130 1.00 0.00
+ATOM 2252 C2' RG3 71 22.970 58.420 31.130 1.00 0.00
+ATOM 2253 1H2' RG3 71 22.520 57.450 30.940 1.00 0.00
+ATOM 2254 O2' RG3 71 22.760 59.350 30.080 1.00 0.00
+ATOM 2255 2HO' RG3 71 23.000 58.930 29.250 1.00 0.00
+ATOM 2256 O3' RG3 71 21.250 59.670 32.300 1.00 0.00
+ATOM 2257 H3T RG3 71 21.130 59.570 31.350 1.00 0.00
+TER
+ENDMDL
diff --git a/regtest/basic/rt-ermsd2/traj.xtc b/regtest/basic/rt-ermsd2/traj.xtc
new file mode 100644
index 0000000000000000000000000000000000000000..fa1e03a04040d79f07b894112432384d07c39e4b
Binary files /dev/null and b/regtest/basic/rt-ermsd2/traj.xtc differ
diff --git a/regtest/basic/rt-hrex-0/out.reference b/regtest/basic/rt-hrex-0/out.reference
index 986db7d35620d38c8b0cd1323235c69c6dbf5396..70fe9f1321d6fa315da012f6b1d2c13ac75eef42 100644
--- a/regtest/basic/rt-hrex-0/out.reference
+++ b/regtest/basic/rt-hrex-0/out.reference
@@ -578,8 +578,8 @@ N C N 1 120.000 585.760 ; Added for Urea (same as N2-CA-N2)
; LINE(512) X X CM HA 4 180.00 4.60240 2 ;
; LINE(513) X X CA H4 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
; LINE(514) X X CA H5 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
-
-
+[ dihedraltypes ]
+; LINE(516) X X X X 9 0.0 1.60247 3 ; fake choice, just here to test gromacs 5.1.4 behavior
[ dihedraltypes ]
;i j k l func
; LINE(519) CT CT OS CT 9 0.0 1.60247 3 ;
diff --git a/regtest/basic/rt-hrex-0/processed.top b/regtest/basic/rt-hrex-0/processed.top
index 88a87338e947e5c45d8b2eba574cbcb4cd48bfe4..5a6a213dd0ea66ff39f326f16bb1f4dbea0619cb 100644
--- a/regtest/basic/rt-hrex-0/processed.top
+++ b/regtest/basic/rt-hrex-0/processed.top
@@ -512,8 +512,8 @@ X X CM H4 4 180.00 4.60240 2 ;
X X CM HA 4 180.00 4.60240 2 ;
X X CA H4 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
X X CA H5 4 180.00 4.60240 2 ; bsd.on C6H6 nmodes
-
-
+[ dihedraltypes ]
+X X X X 9 0.0 1.60247 3 ; fake choice, just here to test gromacs 5.1.4 behavior
[ dihedraltypes ]
;i j k l func
CT CT OS CT 9 0.0 1.60247 3 ;
diff --git a/regtest/basic/rt-make-exceptions/config b/regtest/basic/rt-make-exceptions/config
index 21271768533bba32fce22c032668c452133be719..eb6b0535b390c05e460e947aa44cddf3547562c7 100644
--- a/regtest/basic/rt-make-exceptions/config
+++ b/regtest/basic/rt-make-exceptions/config
@@ -1,2 +1,2 @@
type=make
-plumed_needs="dlopen exceptions"
+plumed_needs="dlopen"
diff --git a/regtest/basic/rt11c/HILLS.0.reference b/regtest/basic/rt11c/HILLS.0.reference
index 0efa61dbdef68594e1a6ba483cc51570de770454..0075bba949b191755f146e8724174094e3e10b16 100644
--- a/regtest/basic/rt11c/HILLS.0.reference
+++ b/regtest/basic/rt11c/HILLS.0.reference
@@ -1,5 +1,6 @@
#! FIELDS time d1 sigma_d1 height biasf
#! SET multivariate false
+#! SET kerneltype gaussian
0.05 1.130546273059004 0.1 0.625 5
0.1 1.097928292824707 0.1 0.59908504146288 5
0.15 1.080244153391634 0.1 0.5771398513895197 5
diff --git a/regtest/basic/rt11c/HILLS.1.reference b/regtest/basic/rt11c/HILLS.1.reference
index a1be29dcf124c3155db27b14ef96b92458c94ef2..27665c087835cdd6ad27fc4103e0037e1b8492fd 100644
--- a/regtest/basic/rt11c/HILLS.1.reference
+++ b/regtest/basic/rt11c/HILLS.1.reference
@@ -1,5 +1,6 @@
#! FIELDS time d2 sigma_d2 height biasf
#! SET multivariate false
+#! SET kerneltype gaussian
0.05 1.203184354540843 0.2 0.625 5
0.1 1.205975816509584 0.2 0.5913730479977681 5
0.15 1.215791771844345 0.2 0.5602906936775773 5
diff --git a/regtest/basic/rt11d/HILLS.0 b/regtest/basic/rt11d/HILLS.0
new file mode 100644
index 0000000000000000000000000000000000000000..0075bba949b191755f146e8724174094e3e10b16
--- /dev/null
+++ b/regtest/basic/rt11d/HILLS.0
@@ -0,0 +1,7 @@
+#! FIELDS time d1 sigma_d1 height biasf
+#! SET multivariate false
+#! SET kerneltype gaussian
+ 0.05 1.130546273059004 0.1 0.625 5
+ 0.1 1.097928292824707 0.1 0.59908504146288 5
+ 0.15 1.080244153391634 0.1 0.5771398513895197 5
+ 0.2 1.086854650075657 0.1 0.5463961934914275 5
diff --git a/regtest/basic/rt11d/HILLS.0.reference b/regtest/basic/rt11d/HILLS.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..0b3e69e2b07574f29de22c5791e844df824dfc9e
--- /dev/null
+++ b/regtest/basic/rt11d/HILLS.0.reference
@@ -0,0 +1,14 @@
+#! FIELDS time d1 sigma_d1 height biasf
+#! SET multivariate false
+#! SET kerneltype gaussian
+ 0.05 1.130546273059004 0.1 0.625 5
+ 0.1 1.097928292824707 0.1 0.59908504146288 5
+ 0.15 1.080244153391634 0.1 0.5771398513895197 5
+ 0.2 1.086854650075657 0.1 0.5463961934914275 5
+#! FIELDS time d1 sigma_d1 height biasf
+#! SET multivariate false
+#! SET kerneltype gaussian
+ 0.05 1.130546273059004 0.1 0.5335854508884743 5
+ 0.1 1.097928292824707 0.1 0.5001031160447613 5
+ 0.15 1.080244153391634 0.1 0.4898375019558275 5
+ 0.2 1.086854650075657 0.1 0.4645277803485113 5
diff --git a/regtest/basic/rt11d/HILLS.1 b/regtest/basic/rt11d/HILLS.1
new file mode 100644
index 0000000000000000000000000000000000000000..27665c087835cdd6ad27fc4103e0037e1b8492fd
--- /dev/null
+++ b/regtest/basic/rt11d/HILLS.1
@@ -0,0 +1,7 @@
+#! FIELDS time d2 sigma_d2 height biasf
+#! SET multivariate false
+#! SET kerneltype gaussian
+ 0.05 1.203184354540843 0.2 0.625 5
+ 0.1 1.205975816509584 0.2 0.5913730479977681 5
+ 0.15 1.215791771844345 0.2 0.5602906936775773 5
+ 0.2 1.223083017342005 0.2 0.539509093634623 5
diff --git a/regtest/basic/rt11d/HILLS.1.reference b/regtest/basic/rt11d/HILLS.1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..aa9cbff8fcf475ee66855a1562bbed20861a2ee5
--- /dev/null
+++ b/regtest/basic/rt11d/HILLS.1.reference
@@ -0,0 +1,14 @@
+#! FIELDS time d2 sigma_d2 height biasf
+#! SET multivariate false
+#! SET kerneltype gaussian
+ 0.05 1.203184354540843 0.2 0.625 5
+ 0.1 1.205975816509584 0.2 0.5913730479977681 5
+ 0.15 1.215791771844345 0.2 0.5602906936775773 5
+ 0.2 1.223083017342005 0.2 0.539509093634623 5
+#! FIELDS time d2 sigma_d2 height biasf
+#! SET multivariate false
+#! SET kerneltype gaussian
+ 0.05 1.203184354540843 0.2 0.5097307624361171 5
+ 0.1 1.205975816509584 0.2 0.4972525338080095 5
+ 0.15 1.215791771844345 0.2 0.4717483444712089 5
+ 0.2 1.223083017342005 0.2 0.4593400817303786 5
diff --git a/regtest/basic/rt11d/Makefile b/regtest/basic/rt11d/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt11d/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt11d/config b/regtest/basic/rt11d/config
new file mode 100644
index 0000000000000000000000000000000000000000..9382cd50db6fe358d77400b91dfc77ebd9b6e4a7
--- /dev/null
+++ b/regtest/basic/rt11d/config
@@ -0,0 +1,4 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f"
+extra_files="../../trajectories/trajectory.xyz"
diff --git a/regtest/basic/rt11d/forces.reference b/regtest/basic/rt11d/forces.reference
new file mode 100644
index 0000000000000000000000000000000000000000..1c7b9490a6953e54de6448978c5705afa58bfc8a
--- /dev/null
+++ b/regtest/basic/rt11d/forces.reference
@@ -0,0 +1,550 @@
+108
+ -5.442374 0.159178 -5.852811
+X -6.881140 -0.143239 7.040617
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 6.881140 0.143239 -7.040617
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.178594 0.186023 0.012128
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X -0.178594 -0.186023 -0.012128
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
+X 0.000000 0.000000 0.000000
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diff --git a/regtest/basic/rt11d/grid0 b/regtest/basic/rt11d/grid0
new file mode 100644
index 0000000000000000000000000000000000000000..b3622f516e14cc62c667dbd6cc20af555cd5dbfe
--- /dev/null
+++ b/regtest/basic/rt11d/grid0
@@ -0,0 +1,1006 @@
+#! FIELDS d1 mdg.bias der_d1
+#! SET min_d1 0
+#! SET max_d1 10
+#! SET nbins_d1 1001
+#! SET periodic_d1 false
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diff --git a/regtest/basic/rt11d/grid0.reference b/regtest/basic/rt11d/grid0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..bac51ca0013b24119f1e6bafac528354a6964b99
--- /dev/null
+++ b/regtest/basic/rt11d/grid0.reference
@@ -0,0 +1,1006 @@
+#! FIELDS d1 mdg.bias der_d1
+#! SET min_d1 0
+#! SET max_d1 10
+#! SET nbins_d1 1001
+#! SET periodic_d1 false
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diff --git a/regtest/basic/rt11d/grid1 b/regtest/basic/rt11d/grid1
new file mode 100644
index 0000000000000000000000000000000000000000..873c5f9da41e351c41f6609eb69f933b02b5810b
--- /dev/null
+++ b/regtest/basic/rt11d/grid1
@@ -0,0 +1,506 @@
+#! FIELDS d2 mdg.bias der_d2
+#! SET min_d2 0
+#! SET max_d2 10
+#! SET nbins_d2 501
+#! SET periodic_d2 false
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diff --git a/regtest/basic/rt11d/grid1.reference b/regtest/basic/rt11d/grid1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..e16355a31afaf55e7c55212dd5f02eb9c8dbed67
--- /dev/null
+++ b/regtest/basic/rt11d/grid1.reference
@@ -0,0 +1,506 @@
+#! FIELDS d2 mdg.bias der_d2
+#! SET min_d2 0
+#! SET max_d2 10
+#! SET nbins_d2 501
+#! SET periodic_d2 false
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diff --git a/regtest/basic/rt11d/plumed.dat b/regtest/basic/rt11d/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..e72f475e143bb693fa08abaec9191d5a84b2435c
--- /dev/null
+++ b/regtest/basic/rt11d/plumed.dat
@@ -0,0 +1,4 @@
+d1: DISTANCE ATOMS=1,10
+d2: DISTANCE ATOMS=50,40
+mdf: PBMETAD ARG=d1,d2 SIGMA=0.1,0.2 HEIGHT=1.0 PACE=10 TEMP=300 BIASFACTOR=5 FILE=HILLS.0,HILLS.1 RESTART=YES
+mdg: PBMETAD ARG=d1,d2 SIGMA=0.1,0.2 HEIGHT=1.0 PACE=10 TEMP=300 BIASFACTOR=5 FILE=HILLS.a,HILLS.b GRID_WFILES=grid0,grid1 GRID_RFILES=grid0,grid1 GRID_WSTRIDE=10 GRID_MIN=0,0 GRID_MAX=10,10 RESTART=YES
diff --git a/regtest/basic/rt11e/GRID.d1.reference b/regtest/basic/rt11e/GRID.d1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..c062273e5f1b99e49f85f954f5d6e0025cbfb9b5
--- /dev/null
+++ b/regtest/basic/rt11e/GRID.d1.reference
@@ -0,0 +1,506 @@
+#! FIELDS d1 mdg.bias der_d1
+#! SET min_d1 0
+#! SET max_d1 10
+#! SET nbins_d1 501
+#! SET periodic_d1 false
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diff --git a/regtest/basic/rt11e/GRID.d2.reference b/regtest/basic/rt11e/GRID.d2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..98fd26024bb22bde520499ecaf8cb05351971a40
--- /dev/null
+++ b/regtest/basic/rt11e/GRID.d2.reference
@@ -0,0 +1,506 @@
+#! FIELDS d2 mdg.bias der_d2
+#! SET min_d2 0
+#! SET max_d2 10
+#! SET nbins_d2 501
+#! SET periodic_d2 false
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diff --git a/regtest/basic/rt11e/HILLS.d1.reference b/regtest/basic/rt11e/HILLS.d1.reference
new file mode 100644
index 0000000000000000000000000000000000000000..ad78a20d99f8dfde757787f24603c135ae1c7519
--- /dev/null
+++ b/regtest/basic/rt11e/HILLS.d1.reference
@@ -0,0 +1,23 @@
+#! FIELDS time d1 sigma_d1_d1 height biasf
+#! SET multivariate true
+#! SET kerneltype gaussian
+#! SET lower_int 0
+#! SET upper_int 8
+ 0.005 1.130546273059004 0.1 0.625 5
+ 0.005 1.080244153391634 0.1 0.625 5
+ 0.01 1.097928292824707 0.1 0.5708373732513973 5
+ 0.01 1.097928292824707 0.1 0.5708373732513973 5
+ 0.015 1.080244153391634 0.1 0.5250895415222568 5
+ 0.015 1.130546273059004 0.1 0.5307193511105233 5
+ 0.02 1.086854650075657 0.1 0.4799150833022805 5
+ 0.02 1.162646040831079 0.1 0.5409665132606842 5
+ 0.025 1.162646040831079 0.1 0.5034646561214069 5
+ 0.025 1.086854650075657 0.1 0.4483431743490295 5
+ 0.03 1.130546273059004 0.1 0.4180104435188454 5
+ 0.03 1.080244153391634 0.1 0.4310651310440506 5
+ 0.035 1.097928292824707 0.1 0.3865728123772332 5
+ 0.035 1.097928292824707 0.1 0.3865728123772332 5
+ 0.04 1.080244153391634 0.1 0.3818954364278632 5
+ 0.04 1.130546273059004 0.1 0.3731960629234151 5
+ 0.045 1.086854650075657 0.1 0.3485621978084766 5
+ 0.045 1.162646040831079 0.1 0.4224288755797881 5
diff --git a/regtest/basic/rt11e/HILLS.d2.reference b/regtest/basic/rt11e/HILLS.d2.reference
new file mode 100644
index 0000000000000000000000000000000000000000..3987be8621ebbc712ad177be9a2375fd680bd785
--- /dev/null
+++ b/regtest/basic/rt11e/HILLS.d2.reference
@@ -0,0 +1,23 @@
+#! FIELDS time d2 sigma_d2_d2 height biasf
+#! SET multivariate true
+#! SET kerneltype gaussian
+#! SET lower_int 0
+#! SET upper_int 8
+ 0.005 1.203184354540843 0.1 0.625 5
+ 0.005 1.215791771844345 0.1 0.625 5
+ 0.01 1.205975816509584 0.1 0.5620221890046579 5
+ 0.01 1.205975816509584 0.1 0.5620221890046579 5
+ 0.015 1.215791771844345 0.1 0.5117892417896344 5
+ 0.015 1.203184354540843 0.1 0.5077380541452163 5
+ 0.02 1.223083017342005 0.1 0.4762245932380713 5
+ 0.02 1.205593428803671 0.1 0.4348488805660838 5
+ 0.025 1.205593428803671 0.1 0.4042544691858879 5
+ 0.025 1.223083017342005 0.1 0.4415820179852334 5
+ 0.03 1.203184354540843 0.1 0.4121136065172801 5
+ 0.03 1.215791771844345 0.1 0.403169946517244 5
+ 0.035 1.205975816509584 0.1 0.3890282714715031 5
+ 0.035 1.205975816509584 0.1 0.3890282714715031 5
+ 0.04 1.215791771844345 0.1 0.3535095388097854 5
+ 0.04 1.203184354540843 0.1 0.3593428964140467 5
+ 0.045 1.223083017342005 0.1 0.3443296404699382 5
+ 0.045 1.205593428803671 0.1 0.2955147991569047 5
diff --git a/regtest/basic/rt11e/Makefile b/regtest/basic/rt11e/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/basic/rt11e/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt11e/config b/regtest/basic/rt11e/config
new file mode 100644
index 0000000000000000000000000000000000000000..758fea0add638b470c99eb007e0aab75ac9956f7
--- /dev/null
+++ b/regtest/basic/rt11e/config
@@ -0,0 +1,4 @@
+mpiprocs=4
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f --multi 2"
diff --git a/regtest/basic/rt11e/forces.0.reference b/regtest/basic/rt11e/forces.0.reference
new file mode 100644
index 0000000000000000000000000000000000000000..3bee2b08c63e4d18770c7ca4021016e553c19042
--- /dev/null
+++ b/regtest/basic/rt11e/forces.0.reference
@@ -0,0 +1,1100 @@
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index 0000000000000000000000000000000000000000..5991a404903f7148c38a48a85344e5d678de2ffe
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diff --git a/regtest/basic/rt11e/plumed.dat b/regtest/basic/rt11e/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..19ea601f5cc0c5261d0860a6c3cf627062e524d5
--- /dev/null
+++ b/regtest/basic/rt11e/plumed.dat
@@ -0,0 +1,3 @@
+d1: DISTANCE ATOMS=1,10
+d2: DISTANCE ATOMS=50,40
+mdg: PBMETAD ARG=d1,d2 SIGMA=1 ADAPTIVE=DIFF SIGMA_MIN=0.1,0.1 HEIGHT=1.0 PACE=1 TEMP=300 BIASFACTOR=5 GRID_WSTRIDE=10 GRID_MIN=0,0 GRID_MAX=10,10 INTERVAL_MIN=0,0 INTERVAL_MAX=8,8 WALKERS_MPI
diff --git a/regtest/basic/rt11e/trajectory.0.xyz b/regtest/basic/rt11e/trajectory.0.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..e9766a03312bd6580f19bf1a8e6242940a4cc7bf
--- /dev/null
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diff --git a/regtest/basic/rt11e/trajectory.1.xyz b/regtest/basic/rt11e/trajectory.1.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..a33fb0241bc304e573b5ca30e71b85e974e0a192
--- /dev/null
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+ Ar 3.37646494012116 1.70006231884180 1.71832858290153
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+ Ar 3.34633106376697 3.34978190801792 2.236597087229162E-002
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+ Ar 3.35993223146283 4.21574688626678 0.855875099815207
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+ Ar 4.16070478480339 4.02326623575585 3.40224115629164
+ Ar 3.41697636966586 4.14568180524404 4.13628183320582
+ 108
+ 5.03880000000000 5.03880000000000 5.03880000000000
+ Ar -3.442612640030015E-002 -3.038146094065802E-003 8.961853877526049E-003
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+ Ar 0.860851777160665 4.089630217237031E-002 2.48983344757901
+ Ar 0.854675871454438 0.842986941975215 1.66825869975346
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+ Ar -8.659954805468062E-002 1.618984616300863E-002 3.35333175349348
+ Ar 0.778131911975841 1.387616841389597E-002 4.21637195948668
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+ Ar 4.408552976870550E-002 1.64473372507317 2.290279582244573E-002
+ Ar 0.778415348285367 1.69954412549695 0.809298967916912
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+ Ar 3.28317357679018 2.54058349516029 0.854165464158608
+ Ar 3.36525900245221 1.68968087928211 1.70274012732660
+ Ar 4.24463681109563 1.68001533846426 2.54613252158648
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+ Ar 3.36961295396958 2.58896311786137 2.50369966409017
+ Ar 3.33685290604760 1.70947949404163 3.38625422076952
+ Ar 4.27405844260463 1.70414008299895 4.26746868193537
+ Ar 4.20512933260014 2.47961626832336 3.37422241474624
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+ Ar 3.35655548830140 3.35872692422093 1.379091017629729E-002
+ Ar 4.23458967291586 3.32768605253125 0.889743784233561
+ Ar 4.11229134987390 4.16680171190873 8.443554208297543E-002
+ Ar 3.36962513427898 4.21182638892354 0.830107614826586
+ Ar 3.37104109525588 3.32449244832513 1.69184596179443
+ Ar 4.14874779473163 3.30138468742149 2.49083991600045
+ Ar 4.18037725617577 4.20262174400839 1.68876604034123
+ Ar 3.27984405172670 4.23678798697386 2.49511534213407
+ Ar 3.33429851464440 3.35707273124879 3.36704782363179
+ Ar 4.24959489972031 3.29512882274164 4.22357684606924
+ Ar 4.17981307035717 4.11282310856903 3.38233134178325
+ Ar 3.39573399684784 4.17462041347496 4.17754464890499
diff --git a/regtest/basic/rt67/config b/regtest/basic/rt67/config
index ce858d0c5a1fc8ff0fa3f73d5836edaf432c82e8..e960f8cb31c6f87fc30d9850689ea8c30e3d3d7b 100644
--- a/regtest/basic/rt67/config
+++ b/regtest/basic/rt67/config
@@ -1,3 +1,3 @@
type=driver
# this is to test a different name
-arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro"
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro --kt 2.494339"
diff --git a/regtest/basic/rt67/plumed.dat b/regtest/basic/rt67/plumed.dat
index 6eed71d034826ddb7913b5f77f947c68276f6605..95c5cd685ecf5e97d5a522c74bf4f1be4f9c3239 100644
--- a/regtest/basic/rt67/plumed.dat
+++ b/regtest/basic/rt67/plumed.dat
@@ -6,7 +6,6 @@ METAD ...
SIGMA=0.20,0.20
HEIGHT=1.20
BIASFACTOR=10
- TEMP=300.0
PACE=500
LABEL=metad
FILE=HILLS
diff --git a/regtest/basic/rt80/HILLS.0.reference b/regtest/basic/rt80/HILLS.0.reference
index e78f843c321f7d72e3be25cd07559dda124e8602..e0600b82e716df924cbdaf0e829cda734ee9dc4e 100644
--- a/regtest/basic/rt80/HILLS.0.reference
+++ b/regtest/basic/rt80/HILLS.0.reference
@@ -1,5 +1,6 @@
#! FIELDS time mu1 sigma_mu1 height biasf
#! SET multivariate false
+#! SET kerneltype gaussian
0.050000 1.130546 0.100000 0.500000 1.000000
0.100000 1.097928 0.100000 0.501269 1.000000
0.150000 1.080244 0.100000 0.500010 1.000000
diff --git a/regtest/basic/rt80/HILLS.1.reference b/regtest/basic/rt80/HILLS.1.reference
index e67d6ebb44cc23a2e1fb8fed14c09927f7157872..5e20f3ea906f15e1f55d00665f2f03742cd62641 100644
--- a/regtest/basic/rt80/HILLS.1.reference
+++ b/regtest/basic/rt80/HILLS.1.reference
@@ -1,5 +1,6 @@
#! FIELDS time phi sigma_phi height biasf
#! SET multivariate false
+#! SET kerneltype gaussian
#! SET min_phi -pi
#! SET max_phi pi
0.050000 0.443934 0.200000 0.500000 1.000000
diff --git a/regtest/crystallization/rt-splane/colv2.reference b/regtest/crystallization/rt-splane/colv2.reference
index 5346af209e6db0ae0f7a088886ce26ad640a86ce..90326673f0ff367216bea889505247e20b66996f 100644
--- a/regtest/crystallization/rt-splane/colv2.reference
+++ b/regtest/crystallization/rt-splane/colv2.reference
@@ -1,12 +1,12 @@
#! FIELDS time s3.mean
- 0.000000 -0.3800
- 1.000000 -0.1411
- 2.000000 -0.4151
- 3.000000 -0.7773
- 4.000000 -0.6901
- 5.000000 -0.6693
- 6.000000 -0.8391
- 7.000000 -0.6999
- 8.000000 -0.5771
- 9.000000 -0.3436
- 10.000000 -0.1871
+ 0.000000 -0.1296
+ 1.000000 -0.0255
+ 2.000000 -0.1883
+ 3.000000 0.0545
+ 4.000000 -0.1441
+ 5.000000 -0.0335
+ 6.000000 -0.0718
+ 7.000000 -0.0869
+ 8.000000 0.0309
+ 9.000000 0.0206
+ 10.000000 -0.0318
diff --git a/regtest/crystallization/rt-splane/forces.reference b/regtest/crystallization/rt-splane/forces.reference
index c79e4d21cd1bfda403556ee754288798e7abbf6e..095a973e8f96664dfd075a42cf575e57accb44a3 100644
--- a/regtest/crystallization/rt-splane/forces.reference
+++ b/regtest/crystallization/rt-splane/forces.reference
@@ -1,5 +1,5 @@
18588
- 9.1352 -2.5139 -4.3405
+ -5.1001 5.2628 5.7010
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -8,9 +8,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -5.6622 -12.4604 -13.4630
-X 2.9410 6.4833 6.9412
-X 2.7149 5.9855 6.4051
+X 1.8248 3.9004 4.2471
+X -1.0443 -2.4172 -2.5576
+X -0.6819 -1.6190 -1.6979
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -88,9 +88,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -3.0882 2.7561 -0.3755
-X 2.7055 -2.1088 0.3248
-X 0.5054 -0.2614 0.0589
+X 4.4080 -3.7231 0.5360
+X -1.6602 1.3722 -0.1975
+X -2.7048 2.2494 -0.3238
X 0.0000 0.0000 0.0000
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X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -0.0606 0.8705 -8.0201
-X 0.0137 -0.3043 4.5844
-X 0.0079 -0.2115 3.5890
+X -0.0669 0.7146 -6.7916
+X -0.0057 -0.2541 3.6016
+X -0.0066 -0.2387 3.4362
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -185899,7 +185899,7 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
18588
- -4.6554 -7.6935 -5.9687
+ -2.0503 -1.0714 0.3891
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -185908,9 +185908,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -3.7745 0.5388 4.1347
-X 1.9417 -0.5343 -1.2503
-X 2.3737 -0.6154 -1.6573
+X 2.3680 -0.5718 -2.1367
+X -1.4723 0.1491 1.4811
+X -0.7657 0.0165 0.8153
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -185988,9 +185988,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -1.1031 -5.6984 3.3033
-X 0.4270 3.1474 -1.7471
-X 0.1780 1.7081 -0.9254
+X -0.2244 -1.0561 0.4448
+X -0.1206 -0.4557 0.1020
+X 0.2447 1.6561 -1.1037
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -186372,9 +186372,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -3.1682 0.7736 1.6076
-X 2.4805 -0.5567 -1.0621
-X 1.0215 -0.2131 -0.3726
+X -3.0671 0.7564 1.5285
+X 2.4701 -0.5477 -1.0886
+X 0.8722 -0.1714 -0.3334
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -187060,9 +187060,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X 0.1287 -2.9648 -0.2904
-X 0.0667 3.7790 0.1855
-X 0.1048 -0.3653 -0.1069
+X 0.0195 -0.3618 -0.0619
+X 0.0029 1.4341 0.0649
+X 0.0239 -0.8395 -0.0956
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -187420,9 +187420,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -2.1390 0.5013 0.5082
-X -1.5273 0.3354 0.2441
-X 3.1382 -0.9298 -1.7706
+X -3.3119 0.8542 1.4953
+X 2.3565 -0.6829 -0.9524
+X 1.2595 -0.3854 -0.4787
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -187492,17 +187492,17 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -0.3165 -0.7789 -0.3806
-X -0.0395 0.0624 -0.0504
-X 0.3109 1.1262 0.3672
+X 0.0939 0.5371 0.1900
+X 0.0254 0.3291 0.1084
+X -0.3064 -0.6783 -0.2871
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X -3.1044 -1.6401 2.1456
-X 2.3419 1.5545 -1.9686
-X 0.6422 0.5575 -0.6846
+X -1.4060 -0.8784 1.1008
+X 1.0795 0.5796 -0.7769
+X 0.1473 0.0328 -0.0727
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
@@ -188100,9 +188100,9 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
-X 0.7002 0.3712 1.0903
-X -0.2617 -0.0446 -0.5254
-X -0.4217 -0.1138 -0.7942
+X 0.7416 0.4569 1.4265
+X -0.8679 -0.2389 -1.2771
+X -0.1628 0.0659 -0.0928
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
diff --git a/regtest/drr/rt-extract/config b/regtest/drr/rt-extract/config
index 6757d601ee4bf1142b95deb0387e289cae4a728f..1d9385ecdf60f22129f9daa3dcf110f870c5266e 100644
--- a/regtest/drr/rt-extract/config
+++ b/regtest/drr/rt-extract/config
@@ -2,14 +2,3 @@ type=plumed
plumed_needs=boost_serialization
plumed_modules=drr
arg="drr_tool --extract test.drrstate -v"
-
-# Skip this since it crashes on travis-ci
-# I'm not sure about the reason, could be the boost version of macports
-function plumed_custom_skip(){
- if [ "$(uname)" == "Darwin" ] ; then
- return 0
- else
- return 1
- fi
-}
-
diff --git a/regtest/drr/rt-merge/config b/regtest/drr/rt-merge/config
index 024e9cfafe4be808201a745e39b784c0c1467dad..94f2c07798c6ef398f13b19b517dc7acaa6d16c1 100644
--- a/regtest/drr/rt-merge/config
+++ b/regtest/drr/rt-merge/config
@@ -1,10 +1,3 @@
-function plumed_custom_skip(){
- if [ "$(uname)" == "Darwin" ] ; then
- return 0
- else
- return 1
- fi
-}
type=plumed
plumed_needs=boost_serialization
plumed_modules=drr
diff --git a/regtest/isdb/rt-cs2backbone-mi/plumed.dat b/regtest/isdb/rt-cs2backbone-mi/plumed.dat
index 3a8650f7d8529aa76adba08e5571f3afde4b6d82..5d43f0fab190a7fabf3c4b92ec7c4f7e6349aae0 100644
--- a/regtest/isdb/rt-cs2backbone-mi/plumed.dat
+++ b/regtest/isdb/rt-cs2backbone-mi/plumed.dat
@@ -4,7 +4,7 @@ d2: DISTANCE ATOMS=10,29
m1: PBMETAD ARG=d1,d2 HEIGHT=0.1 SIGMA=0.2,0.5 PACE=1 TEMP=300 BIASFACTOR=10 FILE=HILLS.0,HILLS.1 WALKERS_MPI
m2: PBMETAD ARG=d1,d2 HEIGHT=0.1 SIGMA=0.2,0.5 PACE=1 TEMP=300 BIASFACTOR=10 FILE=HILLS.0,HILLS.1 WALKERS_MPI
-cs: CS2BACKBONE ATOMS=1-2612 NRES=176 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC
+cs: CS2BACKBONE ATOMS=1-2612 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC
METAINFERENCE ...
ARG=(cs\.ca_.*),(cs\.cb_.*),(cs\.hn_.*),(cs\.nh_.*),m1.bias
@@ -18,7 +18,7 @@ TEMP=300
protein: GROUP ATOMS=1-2612
-csmi: CS2BACKBONE ARG=m2.bias TEMP=300 ATOMS=protein NRES=176 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC DOSCORE REWEIGHT DSIGMA=0 SIGMA_MEAN0=100
+csmi: CS2BACKBONE ARG=m2.bias TEMP=300 ATOMS=protein DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC DOSCORE REWEIGHT DSIGMA=0 SIGMA_MEAN0=100
#csmin: CS2BACKBONE ARG=m2.bias TEMP=300 ATOMS=protein NRES=176 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC DOSCORE REWEIGHT DSIGMA=0 SIGMA_MEAN0=100 NUMERICAL_DERIVATIVES
BIASVALUE ARG=csmi.score
diff --git a/regtest/isdb/rt-cs2backbone-mpi/forces.0.reference b/regtest/isdb/rt-cs2backbone-mpi/forces.0.reference
index 3cb2fb12ddd3aac09c0fafa1b602245ead7ef040..f95cabd3a3b6e6f152e40108d885a77e7020c75d 100644
--- a/regtest/isdb/rt-cs2backbone-mpi/forces.0.reference
+++ b/regtest/isdb/rt-cs2backbone-mpi/forces.0.reference
@@ -1,2 +1,2 @@
-#! FIELDS time cs.ca_1 cs.ca_2 cs.ca_3 cs.ca_4 cs.ca_5 cs.ca_6 cs.ca_7 cs.ca_8 cs.ca_9 cs.ca_10 cs.ca_11 cs.ca_12 cs.ca_13 cs.ca_14 cs.ca_15 cs.ca_16 cs.ca_17 cs.ca_18 cs.ca_19 cs.ca_20 cs.ca_21 cs.ca_22 cs.ca_23 cs.ca_24 cs.ca_25 cs.ca_26 cs.ca_27 cs.ca_28 cs.ca_29 cs.ca_30 cs.ca_31 cs.ca_32 cs.ca_33 cs.ca_34 cs.ca_35 cs.ca_36 cs.ca_37 cs.ca_38 cs.ca_39 cs.ca_40 cs.ca_41 cs.ca_42 cs.ca_43 cs.ca_44 cs.ca_45 cs.ca_46 cs.ca_47 cs.ca_48 cs.ca_49 cs.ca_50 cs.ca_52 cs.ca_53 cs.ca_54 cs.ca_55 cs.ca_56 cs.ca_57 cs.ca_58 cs.ca_59 cs.ca_60 cs.ca_62 cs.ca_63 cs.ca_64 cs.ca_65 cs.ca_66 cs.ca_67 cs.ca_68 cs.ca_69 cs.ca_70 cs.ca_71 cs.ca_72 cs.ca_73 cs.ca_74 cs.ca_75 cs.ca_76 cs.ca_77 cs.ca_78 cs.ca_79 cs.ca_80 cs.ca_81 cs.ca_82 cs.ca_83 cs.ca_84 cs.ca_85 cs.ca_86 cs.ca_87 cs.ca_88 cs.ca_89 cs.ca_90 cs.ca_91 cs.ca_92 cs.ca_93 cs.ca_94 cs.ca_95 cs.ca_96 cs.ca_97 cs.ca_98 cs.ca_99 cs.ca_100 cs.ca_101 cs.ca_102 cs.ca_103 cs.ca_104 cs.ca_105 cs.ca_106 cs.ca_107 cs.ca_108 cs.ca_109 cs.ca_110 cs.ca_111 cs.ca_112 cs.ca_113 cs.ca_115 cs.ca_116 cs.ca_117 cs.ca_118 cs.ca_119 cs.ca_120 cs.ca_121 cs.ca_122 cs.ca_123 cs.ca_124 cs.ca_125 cs.ca_126 cs.ca_127 cs.ca_128 cs.ca_129 cs.ca_130 cs.ca_131 cs.ca_132 cs.ca_133 cs.ca_134 cs.ca_135 cs.ca_136 cs.ca_137 cs.ca_138 cs.ca_139 cs.ca_140 cs.ca_141 cs.ca_142 cs.ca_143 cs.ca_144 cs.ca_145 cs.ca_146 cs.ca_147 cs.ca_148 cs.ca_149 cs.ca_150 cs.ca_151 cs.ca_152 cs.ca_153 cs.ca_154 cs.ca_155 cs.ca_156 cs.ca_157 cs.ca_158 cs.ca_159 cs.ca_161 cs.ca_162 cs.ca_163 cs.ca_166 cs.ca_171 cs.ca_173 cs.ca_174 cs.cb_1 cs.cb_2 cs.cb_4 cs.cb_5 cs.cb_6 cs.cb_7 cs.cb_8 cs.cb_10 cs.cb_11 cs.cb_12 cs.cb_14 cs.cb_16 cs.cb_18 cs.cb_19 cs.cb_20 cs.cb_21 cs.cb_22 cs.cb_23 cs.cb_24 cs.cb_25 cs.cb_26 cs.cb_27 cs.cb_28 cs.cb_30 cs.cb_31 cs.cb_32 cs.cb_33 cs.cb_34 cs.cb_35 cs.cb_36 cs.cb_37 cs.cb_38 cs.cb_39 cs.cb_40 cs.cb_42 cs.cb_43 cs.cb_45 cs.cb_47 cs.cb_48 cs.cb_50 cs.cb_52 cs.cb_54 cs.cb_59 cs.cb_60 cs.cb_65 cs.cb_66 cs.cb_68 cs.cb_70 cs.cb_72 cs.cb_75 cs.cb_76 cs.cb_78 cs.cb_80 cs.cb_81 cs.cb_82 cs.cb_83 cs.cb_84 cs.cb_85 cs.cb_86 cs.cb_87 cs.cb_89 cs.cb_90 cs.cb_92 cs.cb_97 cs.cb_98 cs.cb_99 cs.cb_100 cs.cb_105 cs.cb_106 cs.cb_107 cs.cb_111 cs.cb_112 cs.cb_115 cs.cb_116 cs.cb_117 cs.cb_118 cs.cb_119 cs.cb_120 cs.cb_121 cs.cb_122 cs.cb_124 cs.cb_126 cs.cb_127 cs.cb_128 cs.cb_130 cs.cb_131 cs.cb_132 cs.cb_133 cs.cb_135 cs.cb_136 cs.cb_138 cs.cb_139 cs.cb_140 cs.cb_141 cs.cb_142 cs.cb_143 cs.cb_144 cs.cb_146 cs.cb_147 cs.cb_148 cs.cb_150 cs.cb_151 cs.cb_152 cs.cb_153 cs.cb_154 cs.cb_156 cs.cb_158 cs.cb_159 cs.cb_163 cs.cb_166 cs.cb_167 cs.cb_170 cs.cb_171 cs.cb_173 cs.hn_1 cs.hn_2 cs.hn_4 cs.hn_5 cs.hn_6 cs.hn_7 cs.hn_8 cs.hn_9 cs.hn_10 cs.hn_11 cs.hn_12 cs.hn_13 cs.hn_14 cs.hn_16 cs.hn_17 cs.hn_18 cs.hn_19 cs.hn_20 cs.hn_21 cs.hn_22 cs.hn_23 cs.hn_24 cs.hn_26 cs.hn_27 cs.hn_28 cs.hn_30 cs.hn_31 cs.hn_32 cs.hn_33 cs.hn_34 cs.hn_35 cs.hn_36 cs.hn_37 cs.hn_38 cs.hn_39 cs.hn_40 cs.hn_41 cs.hn_42 cs.hn_43 cs.hn_44 cs.hn_45 cs.hn_46 cs.hn_47 cs.hn_48 cs.hn_49 cs.hn_50 cs.hn_52 cs.hn_53 cs.hn_54 cs.hn_55 cs.hn_56 cs.hn_58 cs.hn_59 cs.hn_60 cs.hn_62 cs.hn_63 cs.hn_64 cs.hn_65 cs.hn_66 cs.hn_67 cs.hn_68 cs.hn_69 cs.hn_70 cs.hn_71 cs.hn_72 cs.hn_73 cs.hn_74 cs.hn_75 cs.hn_76 cs.hn_77 cs.hn_78 cs.hn_79 cs.hn_80 cs.hn_81 cs.hn_82 cs.hn_83 cs.hn_84 cs.hn_85 cs.hn_86 cs.hn_87 cs.hn_88 cs.hn_89 cs.hn_90 cs.hn_91 cs.hn_92 cs.hn_93 cs.hn_95 cs.hn_96 cs.hn_97 cs.hn_98 cs.hn_99 cs.hn_102 cs.hn_103 cs.hn_105 cs.hn_106 cs.hn_107 cs.hn_108 cs.hn_109 cs.hn_110 cs.hn_111 cs.hn_112 cs.hn_113 cs.hn_115 cs.hn_116 cs.hn_117 cs.hn_118 cs.hn_119 cs.hn_120 cs.hn_121 cs.hn_122 cs.hn_123 cs.hn_124 cs.hn_125 cs.hn_126 cs.hn_127 cs.hn_128 cs.hn_129 cs.hn_130 cs.hn_131 cs.hn_132 cs.hn_133 cs.hn_134 cs.hn_135 cs.hn_136 cs.hn_137 cs.hn_138 cs.hn_139 cs.hn_140 cs.hn_141 cs.hn_142 cs.hn_143 cs.hn_144 cs.hn_145 cs.hn_146 cs.hn_147 cs.hn_148 cs.hn_149 cs.hn_150 cs.hn_151 cs.hn_152 cs.hn_153 cs.hn_154 cs.hn_155 cs.hn_156 cs.hn_157 cs.hn_158 cs.hn_159 cs.hn_161 cs.hn_162 cs.hn_163 cs.hn_166 cs.hn_170 cs.hn_171 cs.hn_172 cs.hn_173 cs.hn_174 cs.nh_1 cs.nh_2 cs.nh_4 cs.nh_5 cs.nh_6 cs.nh_7 cs.nh_8 cs.nh_9 cs.nh_10 cs.nh_11 cs.nh_12 cs.nh_13 cs.nh_14 cs.nh_16 cs.nh_17 cs.nh_18 cs.nh_19 cs.nh_20 cs.nh_21 cs.nh_22 cs.nh_23 cs.nh_24 cs.nh_25 cs.nh_26 cs.nh_27 cs.nh_28 cs.nh_30 cs.nh_31 cs.nh_32 cs.nh_33 cs.nh_34 cs.nh_35 cs.nh_36 cs.nh_37 cs.nh_38 cs.nh_39 cs.nh_40 cs.nh_41 cs.nh_42 cs.nh_43 cs.nh_44 cs.nh_45 cs.nh_46 cs.nh_47 cs.nh_48 cs.nh_49 cs.nh_50 cs.nh_52 cs.nh_53 cs.nh_54 cs.nh_55 cs.nh_56 cs.nh_58 cs.nh_59 cs.nh_60 cs.nh_62 cs.nh_63 cs.nh_64 cs.nh_65 cs.nh_66 cs.nh_67 cs.nh_68 cs.nh_69 cs.nh_70 cs.nh_71 cs.nh_72 cs.nh_73 cs.nh_74 cs.nh_75 cs.nh_76 cs.nh_77 cs.nh_78 cs.nh_79 cs.nh_80 cs.nh_81 cs.nh_82 cs.nh_83 cs.nh_84 cs.nh_85 cs.nh_86 cs.nh_87 cs.nh_88 cs.nh_89 cs.nh_90 cs.nh_91 cs.nh_92 cs.nh_93 cs.nh_95 cs.nh_96 cs.nh_97 cs.nh_98 cs.nh_99 cs.nh_102 cs.nh_103 cs.nh_105 cs.nh_106 cs.nh_107 cs.nh_108 cs.nh_109 cs.nh_110 cs.nh_111 cs.nh_112 cs.nh_113 cs.nh_115 cs.nh_116 cs.nh_117 cs.nh_118 cs.nh_119 cs.nh_120 cs.nh_121 cs.nh_122 cs.nh_123 cs.nh_124 cs.nh_126 cs.nh_127 cs.nh_128 cs.nh_129 cs.nh_130 cs.nh_131 cs.nh_132 cs.nh_133 cs.nh_134 cs.nh_135 cs.nh_136 cs.nh_137 cs.nh_138 cs.nh_139 cs.nh_140 cs.nh_141 cs.nh_142 cs.nh_143 cs.nh_144 cs.nh_145 cs.nh_146 cs.nh_147 cs.nh_148 cs.nh_149 cs.nh_150 cs.nh_151 cs.nh_152 cs.nh_153 cs.nh_154 cs.nh_155 cs.nh_156 cs.nh_157 cs.nh_158 cs.nh_159 cs.nh_161 cs.nh_162 cs.nh_163 cs.nh_166 cs.nh_170 cs.nh_171 cs.nh_172 cs.nh_173 cs.nh_174
+#! FIELDS time cs.ca_2 cs.ca_3 cs.ca_4 cs.ca_5 cs.ca_6 cs.ca_7 cs.ca_8 cs.ca_9 cs.ca_10 cs.ca_11 cs.ca_12 cs.ca_13 cs.ca_14 cs.ca_15 cs.ca_16 cs.ca_17 cs.ca_18 cs.ca_19 cs.ca_20 cs.ca_21 cs.ca_22 cs.ca_23 cs.ca_24 cs.ca_25 cs.ca_26 cs.ca_27 cs.ca_28 cs.ca_29 cs.ca_30 cs.ca_31 cs.ca_32 cs.ca_33 cs.ca_34 cs.ca_35 cs.ca_36 cs.ca_37 cs.ca_38 cs.ca_39 cs.ca_40 cs.ca_41 cs.ca_42 cs.ca_43 cs.ca_44 cs.ca_45 cs.ca_46 cs.ca_47 cs.ca_48 cs.ca_49 cs.ca_50 cs.ca_51 cs.ca_53 cs.ca_54 cs.ca_55 cs.ca_56 cs.ca_57 cs.ca_58 cs.ca_59 cs.ca_60 cs.ca_61 cs.ca_63 cs.ca_64 cs.ca_65 cs.ca_66 cs.ca_67 cs.ca_68 cs.ca_69 cs.ca_70 cs.ca_71 cs.ca_72 cs.ca_73 cs.ca_74 cs.ca_75 cs.ca_76 cs.ca_77 cs.ca_78 cs.ca_79 cs.ca_80 cs.ca_81 cs.ca_82 cs.ca_83 cs.ca_84 cs.ca_85 cs.ca_86 cs.ca_87 cs.ca_88 cs.ca_89 cs.ca_90 cs.ca_91 cs.ca_92 cs.ca_93 cs.ca_94 cs.ca_95 cs.ca_96 cs.ca_97 cs.ca_98 cs.ca_99 cs.ca_100 cs.ca_101 cs.ca_102 cs.ca_103 cs.ca_104 cs.ca_105 cs.ca_106 cs.ca_107 cs.ca_108 cs.ca_109 cs.ca_110 cs.ca_111 cs.ca_112 cs.ca_113 cs.ca_114 cs.ca_116 cs.ca_117 cs.ca_118 cs.ca_119 cs.ca_120 cs.ca_121 cs.ca_122 cs.ca_123 cs.ca_124 cs.ca_125 cs.ca_126 cs.ca_127 cs.ca_128 cs.ca_129 cs.ca_130 cs.ca_131 cs.ca_132 cs.ca_133 cs.ca_134 cs.ca_135 cs.ca_136 cs.ca_137 cs.ca_138 cs.ca_139 cs.ca_140 cs.ca_141 cs.ca_142 cs.ca_143 cs.ca_144 cs.ca_145 cs.ca_146 cs.ca_147 cs.ca_148 cs.ca_149 cs.ca_150 cs.ca_151 cs.ca_152 cs.ca_153 cs.ca_154 cs.ca_155 cs.ca_156 cs.ca_157 cs.ca_158 cs.ca_159 cs.ca_160 cs.ca_162 cs.ca_163 cs.ca_164 cs.ca_167 cs.ca_172 cs.ca_174 cs.ca_175 cs.cb_2 cs.cb_3 cs.cb_5 cs.cb_6 cs.cb_7 cs.cb_8 cs.cb_9 cs.cb_11 cs.cb_12 cs.cb_13 cs.cb_15 cs.cb_17 cs.cb_19 cs.cb_20 cs.cb_21 cs.cb_22 cs.cb_23 cs.cb_24 cs.cb_25 cs.cb_26 cs.cb_27 cs.cb_28 cs.cb_29 cs.cb_31 cs.cb_32 cs.cb_33 cs.cb_34 cs.cb_35 cs.cb_36 cs.cb_37 cs.cb_38 cs.cb_39 cs.cb_40 cs.cb_41 cs.cb_43 cs.cb_44 cs.cb_46 cs.cb_48 cs.cb_49 cs.cb_51 cs.cb_53 cs.cb_55 cs.cb_60 cs.cb_61 cs.cb_66 cs.cb_67 cs.cb_69 cs.cb_71 cs.cb_73 cs.cb_76 cs.cb_77 cs.cb_79 cs.cb_81 cs.cb_82 cs.cb_83 cs.cb_84 cs.cb_85 cs.cb_86 cs.cb_87 cs.cb_88 cs.cb_90 cs.cb_91 cs.cb_93 cs.cb_98 cs.cb_99 cs.cb_100 cs.cb_101 cs.cb_106 cs.cb_107 cs.cb_108 cs.cb_112 cs.cb_113 cs.cb_116 cs.cb_117 cs.cb_118 cs.cb_119 cs.cb_120 cs.cb_121 cs.cb_122 cs.cb_123 cs.cb_125 cs.cb_127 cs.cb_128 cs.cb_129 cs.cb_131 cs.cb_132 cs.cb_133 cs.cb_134 cs.cb_136 cs.cb_137 cs.cb_139 cs.cb_140 cs.cb_141 cs.cb_142 cs.cb_143 cs.cb_144 cs.cb_145 cs.cb_147 cs.cb_148 cs.cb_149 cs.cb_151 cs.cb_152 cs.cb_153 cs.cb_154 cs.cb_155 cs.cb_157 cs.cb_159 cs.cb_160 cs.cb_164 cs.cb_167 cs.cb_168 cs.cb_171 cs.cb_172 cs.cb_174 cs.hn_2 cs.hn_3 cs.hn_5 cs.hn_6 cs.hn_7 cs.hn_8 cs.hn_9 cs.hn_10 cs.hn_11 cs.hn_12 cs.hn_13 cs.hn_14 cs.hn_15 cs.hn_17 cs.hn_18 cs.hn_19 cs.hn_20 cs.hn_21 cs.hn_22 cs.hn_23 cs.hn_24 cs.hn_25 cs.hn_27 cs.hn_28 cs.hn_29 cs.hn_31 cs.hn_32 cs.hn_33 cs.hn_34 cs.hn_35 cs.hn_36 cs.hn_37 cs.hn_38 cs.hn_39 cs.hn_40 cs.hn_41 cs.hn_42 cs.hn_43 cs.hn_44 cs.hn_45 cs.hn_46 cs.hn_47 cs.hn_48 cs.hn_49 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diff --git a/regtest/isdb/rt-cs2backbone-mpi/forces.1.reference b/regtest/isdb/rt-cs2backbone-mpi/forces.1.reference
index 0731edd723e63a7f6637f831574a568ecdc993e6..1c9dd44c0570eb1bdfa70227cb71e67eb14c382a 100644
--- a/regtest/isdb/rt-cs2backbone-mpi/forces.1.reference
+++ b/regtest/isdb/rt-cs2backbone-mpi/forces.1.reference
@@ -1,2 +1,2 @@
-#! 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+#! FIELDS time cs.ca_2 cs.ca_3 cs.ca_4 cs.ca_5 cs.ca_6 cs.ca_7 cs.ca_8 cs.ca_9 cs.ca_10 cs.ca_11 cs.ca_12 cs.ca_13 cs.ca_14 cs.ca_15 cs.ca_16 cs.ca_17 cs.ca_18 cs.ca_19 cs.ca_20 cs.ca_21 cs.ca_22 cs.ca_23 cs.ca_24 cs.ca_25 cs.ca_26 cs.ca_27 cs.ca_28 cs.ca_29 cs.ca_30 cs.ca_31 cs.ca_32 cs.ca_33 cs.ca_34 cs.ca_35 cs.ca_36 cs.ca_37 cs.ca_38 cs.ca_39 cs.ca_40 cs.ca_41 cs.ca_42 cs.ca_43 cs.ca_44 cs.ca_45 cs.ca_46 cs.ca_47 cs.ca_48 cs.ca_49 cs.ca_50 cs.ca_51 cs.ca_53 cs.ca_54 cs.ca_55 cs.ca_56 cs.ca_57 cs.ca_58 cs.ca_59 cs.ca_60 cs.ca_61 cs.ca_63 cs.ca_64 cs.ca_65 cs.ca_66 cs.ca_67 cs.ca_68 cs.ca_69 cs.ca_70 cs.ca_71 cs.ca_72 cs.ca_73 cs.ca_74 cs.ca_75 cs.ca_76 cs.ca_77 cs.ca_78 cs.ca_79 cs.ca_80 cs.ca_81 cs.ca_82 cs.ca_83 cs.ca_84 cs.ca_85 cs.ca_86 cs.ca_87 cs.ca_88 cs.ca_89 cs.ca_90 cs.ca_91 cs.ca_92 cs.ca_93 cs.ca_94 cs.ca_95 cs.ca_96 cs.ca_97 cs.ca_98 cs.ca_99 cs.ca_100 cs.ca_101 cs.ca_102 cs.ca_103 cs.ca_104 cs.ca_105 cs.ca_106 cs.ca_107 cs.ca_108 cs.ca_109 cs.ca_110 cs.ca_111 cs.ca_112 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diff --git a/regtest/isdb/rt-cs2backbone-mpi/plumed.dat b/regtest/isdb/rt-cs2backbone-mpi/plumed.dat
index 2864075ba88e3cc0d6b55c488939d04bbe38504b..99c7806c0167634352585d1ae183e732d26c9664 100644
--- a/regtest/isdb/rt-cs2backbone-mpi/plumed.dat
+++ b/regtest/isdb/rt-cs2backbone-mpi/plumed.dat
@@ -1,4 +1,4 @@
-cs: CS2BACKBONE ATOMS=1-2612 NRES=176 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC
+cs: CS2BACKBONE ATOMS=1-2612 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC
ens: ENSEMBLE ARG=(cs\.ca_.*),(cs\.cb_.*),(cs\.hn_.*),(cs\.nh_.*)
diff --git a/regtest/isdb/rt-cs2backbone/colvar.reference b/regtest/isdb/rt-cs2backbone/colvar.reference
index 4bde9f1ae0d9dbed336a6e46dd001c342bd4d6b7..49471c34d216710d3ec1bfd47e87e56e7fd5ddd0 100644
--- a/regtest/isdb/rt-cs2backbone/colvar.reference
+++ b/regtest/isdb/rt-cs2backbone/colvar.reference
@@ -1,2 +1,2 @@
-#! FIELDS time csa cs.ca_1 cs.ca_2 cs.ca_3 cs.ca_4 cs.ca_5 cs.ca_6 cs.ca_7 cs.ca_8 cs.ca_9 cs.ca_10 cs.ca_11 cs.ca_12 cs.ca_13 cs.ca_14 cs.ca_15 cs.ca_16 cs.ca_17 cs.ca_18 cs.ca_19 cs.ca_20 cs.ca_21 cs.ca_22 cs.ca_23 cs.ca_24 cs.ca_25 cs.ca_26 cs.ca_27 cs.ca_28 cs.ca_29 cs.ca_30 cs.ca_31 cs.ca_32 cs.ca_33 cs.ca_34 cs.ca_35 cs.ca_36 cs.ca_37 cs.ca_38 cs.ca_39 cs.ca_40 cs.ca_41 cs.ca_42 cs.ca_43 cs.ca_44 cs.ca_45 cs.ca_46 cs.ca_47 cs.ca_48 cs.ca_49 cs.ca_50 cs.ca_52 cs.ca_53 cs.ca_54 cs.ca_55 cs.ca_56 cs.ca_57 cs.ca_58 cs.ca_59 cs.ca_60 cs.ca_62 cs.ca_63 cs.ca_64 cs.ca_65 cs.ca_66 cs.ca_67 cs.ca_68 cs.ca_69 cs.ca_70 cs.ca_71 cs.ca_72 cs.ca_73 cs.ca_74 cs.ca_75 cs.ca_76 cs.ca_77 cs.ca_78 cs.ca_79 cs.ca_80 cs.ca_81 cs.ca_82 cs.ca_83 cs.ca_84 cs.ca_85 cs.ca_86 cs.ca_87 cs.ca_88 cs.ca_89 cs.ca_90 cs.ca_91 cs.ca_92 cs.ca_93 cs.ca_94 cs.ca_95 cs.ca_96 cs.ca_97 cs.ca_98 cs.ca_99 cs.ca_100 cs.ca_101 cs.ca_102 cs.ca_103 cs.ca_104 cs.ca_105 cs.ca_106 cs.ca_107 cs.ca_108 cs.ca_109 cs.ca_110 cs.ca_111 cs.ca_112 cs.ca_113 cs.ca_115 cs.ca_116 cs.ca_117 cs.ca_118 cs.ca_119 cs.ca_120 cs.ca_121 cs.ca_122 cs.ca_123 cs.ca_124 cs.ca_125 cs.ca_126 cs.ca_127 cs.ca_128 cs.ca_129 cs.ca_130 cs.ca_131 cs.ca_132 cs.ca_133 cs.ca_134 cs.ca_135 cs.ca_136 cs.ca_137 cs.ca_138 cs.ca_139 cs.ca_140 cs.ca_141 cs.ca_142 cs.ca_143 cs.ca_144 cs.ca_145 cs.ca_146 cs.ca_147 cs.ca_148 cs.ca_149 cs.ca_150 cs.ca_151 cs.ca_152 cs.ca_153 cs.ca_154 cs.ca_155 cs.ca_156 cs.ca_157 cs.ca_158 cs.ca_159 cs.ca_161 cs.ca_162 cs.ca_163 cs.ca_166 cs.ca_171 cs.ca_173 cs.ca_174 cs.cb_1 cs.cb_2 cs.cb_4 cs.cb_5 cs.cb_6 cs.cb_7 cs.cb_8 cs.cb_10 cs.cb_11 cs.cb_12 cs.cb_14 cs.cb_16 cs.cb_18 cs.cb_19 cs.cb_20 cs.cb_21 cs.cb_22 cs.cb_23 cs.cb_24 cs.cb_25 cs.cb_26 cs.cb_27 cs.cb_28 cs.cb_30 cs.cb_31 cs.cb_32 cs.cb_33 cs.cb_34 cs.cb_35 cs.cb_36 cs.cb_37 cs.cb_38 cs.cb_39 cs.cb_40 cs.cb_42 cs.cb_43 cs.cb_45 cs.cb_47 cs.cb_48 cs.cb_50 cs.cb_52 cs.cb_54 cs.cb_59 cs.cb_60 cs.cb_65 cs.cb_66 cs.cb_68 cs.cb_70 cs.cb_72 cs.cb_75 cs.cb_76 cs.cb_78 cs.cb_80 cs.cb_81 cs.cb_82 cs.cb_83 cs.cb_84 cs.cb_85 cs.cb_86 cs.cb_87 cs.cb_89 cs.cb_90 cs.cb_92 cs.cb_97 cs.cb_98 cs.cb_99 cs.cb_100 cs.cb_105 cs.cb_106 cs.cb_107 cs.cb_111 cs.cb_112 cs.cb_115 cs.cb_116 cs.cb_117 cs.cb_118 cs.cb_119 cs.cb_120 cs.cb_121 cs.cb_122 cs.cb_124 cs.cb_126 cs.cb_127 cs.cb_128 cs.cb_130 cs.cb_131 cs.cb_132 cs.cb_133 cs.cb_135 cs.cb_136 cs.cb_138 cs.cb_139 cs.cb_140 cs.cb_141 cs.cb_142 cs.cb_143 cs.cb_144 cs.cb_146 cs.cb_147 cs.cb_148 cs.cb_150 cs.cb_151 cs.cb_152 cs.cb_153 cs.cb_154 cs.cb_156 cs.cb_158 cs.cb_159 cs.cb_163 cs.cb_166 cs.cb_167 cs.cb_170 cs.cb_171 cs.cb_173 cs.hn_1 cs.hn_2 cs.hn_4 cs.hn_5 cs.hn_6 cs.hn_7 cs.hn_8 cs.hn_9 cs.hn_10 cs.hn_11 cs.hn_12 cs.hn_13 cs.hn_14 cs.hn_16 cs.hn_17 cs.hn_18 cs.hn_19 cs.hn_20 cs.hn_21 cs.hn_22 cs.hn_23 cs.hn_24 cs.hn_26 cs.hn_27 cs.hn_28 cs.hn_30 cs.hn_31 cs.hn_32 cs.hn_33 cs.hn_34 cs.hn_35 cs.hn_36 cs.hn_37 cs.hn_38 cs.hn_39 cs.hn_40 cs.hn_41 cs.hn_42 cs.hn_43 cs.hn_44 cs.hn_45 cs.hn_46 cs.hn_47 cs.hn_48 cs.hn_49 cs.hn_50 cs.hn_52 cs.hn_53 cs.hn_54 cs.hn_55 cs.hn_56 cs.hn_58 cs.hn_59 cs.hn_60 cs.hn_62 cs.hn_63 cs.hn_64 cs.hn_65 cs.hn_66 cs.hn_67 cs.hn_68 cs.hn_69 cs.hn_70 cs.hn_71 cs.hn_72 cs.hn_73 cs.hn_74 cs.hn_75 cs.hn_76 cs.hn_77 cs.hn_78 cs.hn_79 cs.hn_80 cs.hn_81 cs.hn_82 cs.hn_83 cs.hn_84 cs.hn_85 cs.hn_86 cs.hn_87 cs.hn_88 cs.hn_89 cs.hn_90 cs.hn_91 cs.hn_92 cs.hn_93 cs.hn_95 cs.hn_96 cs.hn_97 cs.hn_98 cs.hn_99 cs.hn_102 cs.hn_103 cs.hn_105 cs.hn_106 cs.hn_107 cs.hn_108 cs.hn_109 cs.hn_110 cs.hn_111 cs.hn_112 cs.hn_113 cs.hn_115 cs.hn_116 cs.hn_117 cs.hn_118 cs.hn_119 cs.hn_120 cs.hn_121 cs.hn_122 cs.hn_123 cs.hn_124 cs.hn_125 cs.hn_126 cs.hn_127 cs.hn_128 cs.hn_129 cs.hn_130 cs.hn_131 cs.hn_132 cs.hn_133 cs.hn_134 cs.hn_135 cs.hn_136 cs.hn_137 cs.hn_138 cs.hn_139 cs.hn_140 cs.hn_141 cs.hn_142 cs.hn_143 cs.hn_144 cs.hn_145 cs.hn_146 cs.hn_147 cs.hn_148 cs.hn_149 cs.hn_150 cs.hn_151 cs.hn_152 cs.hn_153 cs.hn_154 cs.hn_155 cs.hn_156 cs.hn_157 cs.hn_158 cs.hn_159 cs.hn_161 cs.hn_162 cs.hn_163 cs.hn_166 cs.hn_170 cs.hn_171 cs.hn_172 cs.hn_173 cs.hn_174 cs.nh_1 cs.nh_2 cs.nh_4 cs.nh_5 cs.nh_6 cs.nh_7 cs.nh_8 cs.nh_9 cs.nh_10 cs.nh_11 cs.nh_12 cs.nh_13 cs.nh_14 cs.nh_16 cs.nh_17 cs.nh_18 cs.nh_19 cs.nh_20 cs.nh_21 cs.nh_22 cs.nh_23 cs.nh_24 cs.nh_25 cs.nh_26 cs.nh_27 cs.nh_28 cs.nh_30 cs.nh_31 cs.nh_32 cs.nh_33 cs.nh_34 cs.nh_35 cs.nh_36 cs.nh_37 cs.nh_38 cs.nh_39 cs.nh_40 cs.nh_41 cs.nh_42 cs.nh_43 cs.nh_44 cs.nh_45 cs.nh_46 cs.nh_47 cs.nh_48 cs.nh_49 cs.nh_50 cs.nh_52 cs.nh_53 cs.nh_54 cs.nh_55 cs.nh_56 cs.nh_58 cs.nh_59 cs.nh_60 cs.nh_62 cs.nh_63 cs.nh_64 cs.nh_65 cs.nh_66 cs.nh_67 cs.nh_68 cs.nh_69 cs.nh_70 cs.nh_71 cs.nh_72 cs.nh_73 cs.nh_74 cs.nh_75 cs.nh_76 cs.nh_77 cs.nh_78 cs.nh_79 cs.nh_80 cs.nh_81 cs.nh_82 cs.nh_83 cs.nh_84 cs.nh_85 cs.nh_86 cs.nh_87 cs.nh_88 cs.nh_89 cs.nh_90 cs.nh_91 cs.nh_92 cs.nh_93 cs.nh_95 cs.nh_96 cs.nh_97 cs.nh_98 cs.nh_99 cs.nh_102 cs.nh_103 cs.nh_105 cs.nh_106 cs.nh_107 cs.nh_108 cs.nh_109 cs.nh_110 cs.nh_111 cs.nh_112 cs.nh_113 cs.nh_115 cs.nh_116 cs.nh_117 cs.nh_118 cs.nh_119 cs.nh_120 cs.nh_121 cs.nh_122 cs.nh_123 cs.nh_124 cs.nh_126 cs.nh_127 cs.nh_128 cs.nh_129 cs.nh_130 cs.nh_131 cs.nh_132 cs.nh_133 cs.nh_134 cs.nh_135 cs.nh_136 cs.nh_137 cs.nh_138 cs.nh_139 cs.nh_140 cs.nh_141 cs.nh_142 cs.nh_143 cs.nh_144 cs.nh_145 cs.nh_146 cs.nh_147 cs.nh_148 cs.nh_149 cs.nh_150 cs.nh_151 cs.nh_152 cs.nh_153 cs.nh_154 cs.nh_155 cs.nh_156 cs.nh_157 cs.nh_158 cs.nh_159 cs.nh_161 cs.nh_162 cs.nh_163 cs.nh_166 cs.nh_170 cs.nh_171 cs.nh_172 cs.nh_173 cs.nh_174
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+#! 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cs.expca_122 cs.expca_123 cs.expca_124 cs.expca_125 cs.expca_126 cs.expca_127 cs.expca_128 cs.expca_129 cs.expca_130 cs.expca_131 cs.expca_132 cs.expca_133 cs.expca_134 cs.expca_135 cs.expca_136 cs.expca_137 cs.expca_138 cs.expca_139 cs.expca_140 cs.expca_141 cs.expca_142 cs.expca_143 cs.expca_144 cs.expca_145 cs.expca_146 cs.expca_147 cs.expca_148 cs.expca_149 cs.expca_150 cs.expca_151 cs.expca_152 cs.expca_153 cs.expca_154 cs.expca_155 cs.expca_156 cs.expca_157 cs.expca_158 cs.expca_159 cs.expca_160 cs.expca_162 cs.expca_163 cs.expca_164 cs.expca_167 cs.expca_172 cs.expca_174 cs.expca_175 cs.expcb_2 cs.expcb_3 cs.expcb_5 cs.expcb_6 cs.expcb_7 cs.expcb_8 cs.expcb_9 cs.expcb_11 cs.expcb_12 cs.expcb_13 cs.expcb_15 cs.expcb_17 cs.expcb_19 cs.expcb_20 cs.expcb_21 cs.expcb_22 cs.expcb_23 cs.expcb_24 cs.expcb_25 cs.expcb_26 cs.expcb_27 cs.expcb_28 cs.expcb_29 cs.expcb_31 cs.expcb_32 cs.expcb_33 cs.expcb_34 cs.expcb_35 cs.expcb_36 cs.expcb_37 cs.expcb_38 cs.expcb_39 cs.expcb_40 cs.expcb_41 cs.expcb_43 cs.expcb_44 cs.expcb_46 cs.expcb_48 cs.expcb_49 cs.expcb_51 cs.expcb_53 cs.expcb_55 cs.expcb_60 cs.expcb_61 cs.expcb_66 cs.expcb_67 cs.expcb_69 cs.expcb_71 cs.expcb_73 cs.expcb_76 cs.expcb_77 cs.expcb_79 cs.expcb_81 cs.expcb_82 cs.expcb_83 cs.expcb_84 cs.expcb_85 cs.expcb_86 cs.expcb_87 cs.expcb_88 cs.expcb_90 cs.expcb_91 cs.expcb_93 cs.expcb_98 cs.expcb_99 cs.expcb_100 cs.expcb_101 cs.expcb_106 cs.expcb_107 cs.expcb_108 cs.expcb_112 cs.expcb_113 cs.expcb_116 cs.expcb_117 cs.expcb_118 cs.expcb_119 cs.expcb_120 cs.expcb_121 cs.expcb_122 cs.expcb_123 cs.expcb_125 cs.expcb_127 cs.expcb_128 cs.expcb_129 cs.expcb_131 cs.expcb_132 cs.expcb_133 cs.expcb_134 cs.expcb_136 cs.expcb_137 cs.expcb_139 cs.expcb_140 cs.expcb_141 cs.expcb_142 cs.expcb_143 cs.expcb_144 cs.expcb_145 cs.expcb_147 cs.expcb_148 cs.expcb_149 cs.expcb_151 cs.expcb_152 cs.expcb_153 cs.expcb_154 cs.expcb_155 cs.expcb_157 cs.expcb_159 cs.expcb_160 cs.expcb_164 cs.expcb_167 cs.expcb_168 cs.expcb_171 cs.expcb_172 cs.expcb_174 cs.exphn_2 cs.exphn_3 cs.exphn_5 cs.exphn_6 cs.exphn_7 cs.exphn_8 cs.exphn_9 cs.exphn_10 cs.exphn_11 cs.exphn_12 cs.exphn_13 cs.exphn_14 cs.exphn_15 cs.exphn_17 cs.exphn_18 cs.exphn_19 cs.exphn_20 cs.exphn_21 cs.exphn_22 cs.exphn_23 cs.exphn_24 cs.exphn_25 cs.exphn_27 cs.exphn_28 cs.exphn_29 cs.exphn_31 cs.exphn_32 cs.exphn_33 cs.exphn_34 cs.exphn_35 cs.exphn_36 cs.exphn_37 cs.exphn_38 cs.exphn_39 cs.exphn_40 cs.exphn_41 cs.exphn_42 cs.exphn_43 cs.exphn_44 cs.exphn_45 cs.exphn_46 cs.exphn_47 cs.exphn_48 cs.exphn_49 cs.exphn_50 cs.exphn_51 cs.exphn_53 cs.exphn_54 cs.exphn_55 cs.exphn_56 cs.exphn_57 cs.exphn_59 cs.exphn_60 cs.exphn_61 cs.exphn_63 cs.exphn_64 cs.exphn_65 cs.exphn_66 cs.exphn_67 cs.exphn_68 cs.exphn_69 cs.exphn_70 cs.exphn_71 cs.exphn_72 cs.exphn_73 cs.exphn_74 cs.exphn_75 cs.exphn_76 cs.exphn_77 cs.exphn_78 cs.exphn_79 cs.exphn_80 cs.exphn_81 cs.exphn_82 cs.exphn_83 cs.exphn_84 cs.exphn_85 cs.exphn_86 cs.exphn_87 cs.exphn_88 cs.exphn_89 cs.exphn_90 cs.exphn_91 cs.exphn_92 cs.exphn_93 cs.exphn_94 cs.exphn_96 cs.exphn_97 cs.exphn_98 cs.exphn_99 cs.exphn_100 cs.exphn_103 cs.exphn_104 cs.exphn_106 cs.exphn_107 cs.exphn_108 cs.exphn_109 cs.exphn_110 cs.exphn_111 cs.exphn_112 cs.exphn_113 cs.exphn_114 cs.exphn_116 cs.exphn_117 cs.exphn_118 cs.exphn_119 cs.exphn_120 cs.exphn_121 cs.exphn_122 cs.exphn_123 cs.exphn_124 cs.exphn_125 cs.exphn_126 cs.exphn_127 cs.exphn_128 cs.exphn_129 cs.exphn_130 cs.exphn_131 cs.exphn_132 cs.exphn_133 cs.exphn_134 cs.exphn_135 cs.exphn_136 cs.exphn_137 cs.exphn_138 cs.exphn_139 cs.exphn_140 cs.exphn_141 cs.exphn_142 cs.exphn_143 cs.exphn_144 cs.exphn_145 cs.exphn_146 cs.exphn_147 cs.exphn_148 cs.exphn_149 cs.exphn_150 cs.exphn_151 cs.exphn_152 cs.exphn_153 cs.exphn_154 cs.exphn_155 cs.exphn_156 cs.exphn_157 cs.exphn_158 cs.exphn_159 cs.exphn_160 cs.exphn_162 cs.exphn_163 cs.exphn_164 cs.exphn_167 cs.exphn_171 cs.exphn_172 cs.exphn_173 cs.exphn_174 cs.exphn_175 cs.expnh_2 cs.expnh_3 cs.expnh_5 cs.expnh_6 cs.expnh_7 cs.expnh_8 cs.expnh_9 cs.expnh_10 cs.expnh_11 cs.expnh_12 cs.expnh_13 cs.expnh_14 cs.expnh_15 cs.expnh_17 cs.expnh_18 cs.expnh_19 cs.expnh_20 cs.expnh_21 cs.expnh_22 cs.expnh_23 cs.expnh_24 cs.expnh_25 cs.expnh_26 cs.expnh_27 cs.expnh_28 cs.expnh_29 cs.expnh_31 cs.expnh_32 cs.expnh_33 cs.expnh_34 cs.expnh_35 cs.expnh_36 cs.expnh_37 cs.expnh_38 cs.expnh_39 cs.expnh_40 cs.expnh_41 cs.expnh_42 cs.expnh_43 cs.expnh_44 cs.expnh_45 cs.expnh_46 cs.expnh_47 cs.expnh_48 cs.expnh_49 cs.expnh_50 cs.expnh_51 cs.expnh_53 cs.expnh_54 cs.expnh_55 cs.expnh_56 cs.expnh_57 cs.expnh_59 cs.expnh_60 cs.expnh_61 cs.expnh_63 cs.expnh_64 cs.expnh_65 cs.expnh_66 cs.expnh_67 cs.expnh_68 cs.expnh_69 cs.expnh_70 cs.expnh_71 cs.expnh_72 cs.expnh_73 cs.expnh_74 cs.expnh_75 cs.expnh_76 cs.expnh_77 cs.expnh_78 cs.expnh_79 cs.expnh_80 cs.expnh_81 cs.expnh_82 cs.expnh_83 cs.expnh_84 cs.expnh_85 cs.expnh_86 cs.expnh_87 cs.expnh_88 cs.expnh_89 cs.expnh_90 cs.expnh_91 cs.expnh_92 cs.expnh_93 cs.expnh_94 cs.expnh_96 cs.expnh_97 cs.expnh_98 cs.expnh_99 cs.expnh_100 cs.expnh_103 cs.expnh_104 cs.expnh_106 cs.expnh_107 cs.expnh_108 cs.expnh_109 cs.expnh_110 cs.expnh_111 cs.expnh_112 cs.expnh_113 cs.expnh_114 cs.expnh_116 cs.expnh_117 cs.expnh_118 cs.expnh_119 cs.expnh_120 cs.expnh_121 cs.expnh_122 cs.expnh_123 cs.expnh_124 cs.expnh_125 cs.expnh_127 cs.expnh_128 cs.expnh_129 cs.expnh_130 cs.expnh_131 cs.expnh_132 cs.expnh_133 cs.expnh_134 cs.expnh_135 cs.expnh_136 cs.expnh_137 cs.expnh_138 cs.expnh_139 cs.expnh_140 cs.expnh_141 cs.expnh_142 cs.expnh_143 cs.expnh_144 cs.expnh_145 cs.expnh_146 cs.expnh_147 cs.expnh_148 cs.expnh_149 cs.expnh_150 cs.expnh_151 cs.expnh_152 cs.expnh_153 cs.expnh_154 cs.expnh_155 cs.expnh_156 cs.expnh_157 cs.expnh_158 cs.expnh_159 cs.expnh_160 cs.expnh_162 cs.expnh_163 cs.expnh_164 cs.expnh_167 cs.expnh_171 cs.expnh_172 cs.expnh_173 cs.expnh_174 cs.expnh_175
+ 0.000000 1013.7762 62.0730 52.3706 64.4137 59.7863 60.6879 56.4595 56.0189 54.5454 59.4599 51.2394 61.2660 54.6233 44.3991 53.6047 62.8787 55.2518 44.2747 54.7131 60.9540 55.9041 56.8460 55.1113 53.3852 57.3596 52.2858 55.6175 57.6336 53.6239 64.1857 59.1132 66.8493 55.7794 59.1292 55.0374 60.1025 58.8113 53.1038 56.0572 62.2068 63.4757 45.1819 59.3763 56.6704 44.5722 54.6029 44.9747 56.6078 59.5705 45.0354 60.4493 58.9363 47.1741 55.0026 59.9832 60.2715 62.1029 45.2073 57.6760 53.4603 55.3549 42.8546 42.5432 54.1798 54.6084 62.7618 55.5677 46.0571 52.5093 44.6140 62.5575 46.5935 45.1526 55.6616 56.6487 61.8745 55.7714 42.8489 59.9596 53.4024 54.6861 55.3909 56.1854 57.8877 52.5591 57.1525 64.5239 52.4386 54.6889 47.4524 62.0905 44.6840 62.0626 47.0500 59.8543 53.0972 56.3258 52.8093 53.3313 51.0327 50.5406 42.9156 62.4402 54.7643 59.5677 53.4653 44.6307 56.9849 57.1094 56.4790 54.5636 58.8532 60.8029 50.6872 58.2398 58.9570 59.6962 62.1340 56.3216 55.7682 45.6923 54.5934 46.7144 61.6256 62.6774 57.4535 44.6239 54.1576 63.4026 57.6458 54.4580 45.2629 58.4273 55.3277 62.9301 65.4181 59.9661 53.9957 57.6088 57.9670 57.9326 57.2349 43.3458 55.5668 60.0078 54.7210 44.1874 56.3149 59.1342 57.8373 53.6586 56.1674 60.7704 59.6696 60.7819 51.6383 51.7341 44.0541 55.4662 53.8065 56.7795 54.2547 53.5108 42.7161 34.2937 38.9559 71.7660 34.8127 42.2615 42.6553 39.8590 21.4642 34.0789 38.3226 31.2951 43.6700 32.1148 34.0880 65.4524 42.6126 32.8132 43.4997 37.4657 18.2169 39.0673 33.9617 42.3412 31.5770 68.1900 18.4224 29.1037 37.8974 39.6410 30.5450 18.7755 41.6034 63.1973 68.7844 29.3334 30.2885 40.9613 39.1245 30.4924 64.2948 35.9660 32.1716 41.9359 33.7734 39.1255 38.6119 31.7084 39.5749 69.6243 35.1265 65.8722 37.9460 29.6275 36.1351 42.1447 30.7567 40.4355 31.0297 42.1361 40.1515 42.9276 35.9857 71.0150 43.1114 65.8322 32.5373 18.9061 36.3863 69.8383 38.8008 43.1785 42.1500 69.1031 21.0233 32.4623 68.9980 29.7404 28.1435 40.7358 40.0967 35.0409 34.0597 31.3908 42.0009 35.3772 31.6183 33.6728 32.0497 31.2342 38.1085 31.1480 29.1712 18.3978 32.6398 29.8797 29.9299 38.5390 66.6853 28.9447 38.8034 31.8682 69.4484 63.3771 35.8460 32.2684 71.7774 19.5422 44.0455 45.3084 65.5408 39.6278 44.2547 41.4515 19.3336 8.3956 8.1848 8.6158 8.4258 8.4709 9.3888 9.4444 9.3433 9.2101 8.5786 9.3666 7.9867 7.6985 9.1791 7.8827 8.2093 8.8014 8.1572 9.2300 9.0427 8.5182 8.8400 8.2006 7.7422 8.0822 8.9440 9.5478 8.2073 7.6799 8.0440 7.6348 8.4802 8.0264 7.6663 7.9577 7.5794 7.4226 7.9847 8.1008 7.6811 6.8613 8.2277 8.0954 7.8048 9.0453 8.6393 8.9681 7.9238 7.6758 9.1173 9.0910 9.7445 8.3904 8.2988 9.4149 8.3619 8.2689 9.6085 7.4959 7.7449 8.4161 8.0767 7.9356 9.1390 8.1650 8.4150 8.3073 6.5523 8.3250 8.6975 7.7499 7.5113 8.9392 7.9568 8.5391 9.4452 8.7498 9.0756 7.9118 8.1422 7.5522 8.3382 8.5531 9.7142 8.2704 8.0184 9.4378 7.4284 8.0328 8.1573 8.7344 8.7015 7.7948 9.4030 8.4866 7.5671 8.4926 8.5786 8.1205 8.5526 9.1677 8.8688 8.9762 8.0568 8.4637 8.3728 8.3783 8.0683 7.4686 7.9969 8.9155 7.6074 8.5530 8.2950 8.5958 8.8931 7.1535 8.7365 9.2700 8.7580 7.9432 8.7734 8.1949 8.1992 7.7894 7.8197 8.0927 7.7994 7.5572 8.2136 7.7122 8.0369 7.5493 8.5914 8.7952 8.1163 8.3927 8.0338 8.6052 9.2808 7.7869 8.6136 8.8987 8.5515 8.4698 8.8166 8.1780 6.4731 8.4875 8.5228 8.2109 8.9355 8.5985 7.0547 8.0462 8.3482 116.6918 121.9062 114.8220 119.9097 121.5690 121.6931 130.2132 125.6208 130.5275 122.4980 126.2708 109.6879 120.4056 126.1067 106.7693 122.4414 121.7389 118.0299 121.7100 124.5624 124.7386 122.5234 126.5566 119.2430 118.2675 120.1204 120.3851 120.9825 121.9306 120.6263 117.5530 119.4497 116.7107 119.1598 119.0635 116.5841 107.6017 109.7018 121.1796 119.2702 109.3037 112.2750 103.9334 115.7907 126.7110 115.9154 120.1176 125.7704 114.6887 122.0560 125.3974 129.2830 112.5522 120.4731 115.2584 126.9208 109.2336 109.7778 123.1069 117.5301 111.6849 119.2762 109.9256 113.6238 107.2713 110.6054 113.5356 113.1287 121.9717 115.4850 113.4984 115.5951 107.4014 123.0122 114.1364 117.5227 118.8666 123.1010 126.3742 117.0101 117.7327 123.3504 121.2959 121.6423 115.4650 109.2847 111.8720 112.0057 118.4960 125.8575 120.0978 123.2555 121.4647 110.8560 121.4479 113.0550 121.9223 110.3643 113.8355 123.4550 122.0488 117.4141 119.6662 116.4161 122.5649 125.3708 114.8163 126.9575 115.9813 120.4407 124.5692 111.9737 118.9638 121.5864 128.5934 121.6842 106.8831 121.7053 125.4221 128.3906 117.8737 111.0562 119.3753 116.2936 118.4522 122.6199 119.6260 121.3386 117.0253 114.4167 116.4174 116.7625 104.7602 113.5643 124.0201 117.2104 109.6820 122.4872 115.3610 116.3335 118.3537 122.7614 129.0059 117.9062 122.6280 126.7315 113.0731 107.3245 125.3253 123.5263 115.4587 120.3210 117.9950 114.7509 124.4085 107.8531 61.4720 51.0640 62.6960 60.5430 58.6900 55.6380 53.2260 54.7270 57.9980 50.7080 60.5410 55.6210 45.2100 52.7460 64.7290 55.4100 45.1840 54.9390 59.9140 55.2170 55.5360 55.1110 51.5510 54.4410 54.3260 55.2180 56.1830 58.1550 66.0720 60.4030 67.1550 55.8810 57.7310 56.5810 61.5650 60.3620 54.3510 57.0840 62.3830 62.7180 45.6680 58.4110 53.9960 44.5910 53.9450 45.4490 57.5910 61.0090 45.1660 58.8470 58.0330 56.7110 54.4770 61.3870 57.6420 62.7250 44.9770 56.0910 54.4950 54.5020 44.8770 46.5280 51.4590 55.8280 61.7580 55.0070 57.0790 52.0970 45.0160 61.5920 45.0720 43.2780 55.8090 56.4820 63.7330 55.9500 43.5870 61.1790 53.4410 55.9880 56.3590 54.3650 60.1300 52.5700 55.6430 64.8350 54.0370 54.5280 56.6650 63.1390 45.6260 62.6450 45.0410 59.4580 53.1490 54.8580 53.7720 51.5260 53.8380 49.9740 43.4690 63.7740 54.0800 60.3960 55.4210 46.3000 57.3270 58.2400 55.6730 55.6440 58.6210 60.6750 50.6310 57.8170 57.1280 59.3260 60.1030 54.1540 55.6450 44.8380 56.3860 54.8270 63.8620 63.4810 56.1340 46.5710 54.6860 63.7860 56.7150 55.2000 46.0090 56.7200 55.9510 61.2320 65.8830 59.0550 54.7730 59.4810 59.0100 57.5220 57.7980 43.9260 58.2230 59.5820 52.2380 44.7080 57.2020 59.9580 58.6670 54.6690 56.3880 59.1950 59.2290 60.7690 54.1800 52.6470 45.3310 54.8060 54.6520 58.3120 54.9050 52.5170 45.0200 33.0890 37.6620 70.7380 36.1430 42.9950 42.8410 41.1400 22.6520 33.2760 39.7070 30.2790 43.9600 33.3220 35.0330 66.4650 42.5620 31.4670 42.9630 35.9230 18.8650 38.7940 36.1520 31.6380 32.4080 68.5410 18.2600 27.9510 39.4480 40.4230 29.9100 18.2430 41.4080 62.8480 69.3860 30.0700 30.2630 39.4510 38.4700 31.2240 64.7700 38.8320 33.2990 39.4150 35.6860 38.6930 39.0780 31.6470 39.7820 70.5550 34.6750 69.8450 39.0040 30.0660 37.1070 41.2340 29.2410 40.6860 31.6480 39.2930 38.9430 41.7530 34.5660 69.3040 44.1360 63.8500 31.1040 19.6160 37.0250 69.0700 39.9820 43.2360 43.4030 66.7940 22.8250 32.8180 68.5860 28.9690 27.1470 38.9540 39.1440 35.3050 33.4060 31.2580 42.0740 35.7660 32.5740 33.6220 32.6650 30.0440 35.8540 30.9950 29.4390 18.1280 33.5880 30.3220 29.4490 38.9250 65.5200 29.6170 38.2470 32.3520 71.2740 63.5050 38.5870 32.0780 72.4060 19.1490 43.5460 43.1540 63.8580 39.6270 43.3660 42.6050 18.9580 8.5450 8.7690 8.7780 8.6390 8.9150 9.5410 9.2360 9.0260 9.5950 8.8780 9.8660 8.5420 8.0010 9.1560 7.2040 8.3840 9.3480 8.7840 9.4300 8.6310 8.1630 8.8880 8.9780 7.5150 8.3670 10.6400 10.3000 9.1980 8.0200 7.1100 7.0570 8.8700 8.6060 8.2630 7.8900 7.9370 7.5380 8.0050 9.1200 7.9110 6.3950 7.7090 6.8100 8.4340 9.4960 8.3710 8.7820 7.5240 6.8970 9.2340 8.5140 9.7790 8.1050 7.8950 9.4380 7.1770 9.2030 9.9350 6.5070 7.2540 8.5960 6.5880 7.4550 9.4480 7.7820 8.4500 8.0470 6.9750 7.6730 8.6030 8.0980 6.9810 9.1570 7.7760 9.0740 9.1260 8.5260 9.4540 7.0300 8.3510 8.2740 7.7850 8.0380 10.7200 7.2230 7.5160 9.1940 6.7440 7.8050 8.0560 8.4710 8.4180 7.9050 8.7250 10.0700 7.1140 9.3780 8.6530 8.1940 8.1260 9.7960 9.1450 8.9870 7.5880 8.8220 7.4600 9.3780 7.2790 6.9260 7.5660 9.5620 7.8180 7.4880 8.3530 9.4510 8.1420 7.3780 8.2560 8.9820 9.3910 7.5100 8.7040 8.8830 8.8990 7.5970 7.2300 8.2960 7.4880 8.2430 7.8500 6.9420 7.6010 7.5050 8.2530 8.8890 7.8290 8.0290 7.5690 8.8830 9.4200 7.5100 8.7510 9.6330 9.2190 8.5400 8.8280 8.0300 6.8120 9.0830 8.5450 8.6580 8.7370 8.2810 7.1170 8.1740 8.2790 123.4380 127.2310 114.9860 123.5130 119.0290 117.0090 124.2580 124.3630 132.6970 118.5450 131.1950 101.6270 123.3480 126.2910 102.6400 121.2850 127.0200 120.5760 118.6680 123.0620 122.4700 125.0110 129.3670 114.4340 118.0550 115.9960 124.2280 124.3130 125.8580 117.2330 115.5730 118.1500 121.2360 119.3090 120.7260 119.4920 108.5450 108.1640 118.7150 118.6590 105.7690 113.7700 104.7030 113.7020 124.9760 118.1590 116.5560 123.7170 119.1680 125.0050 127.6540 127.6060 114.2890 119.8440 110.7210 127.7770 110.2670 106.0980 124.0050 116.1360 109.2500 122.2640 111.1940 112.6170 110.2540 111.5560 113.9570 108.6690 115.4460 114.6570 111.5880 121.0420 106.2700 124.3630 110.9550 116.5670 119.4700 118.8230 132.3880 106.9260 112.8880 120.0700 117.3560 118.8920 122.7600 110.6690 107.7220 110.9860 121.3790 130.5590 120.3800 123.3020 123.5440 109.2080 119.1650 110.0320 119.3970 110.7040 116.8910 124.4040 119.1930 115.8630 118.4750 115.4490 122.7710 120.1770 119.5200 125.0210 118.9060 119.8010 122.9450 111.9440 115.5550 124.6780 133.2240 118.0600 110.9240 115.1970 124.1440 131.9220 118.7080 108.0380 122.8430 114.7480 124.4920 122.0760 117.3550 121.2570 117.9030 116.9690 114.2140 115.5040 104.7860 110.2550 120.6700 111.1120 110.9660 119.8140 117.0670 116.8420 119.4610 121.5650 134.7750 116.9770 121.4830 132.4770 111.5750 104.3120 121.0920 126.0960 115.6510 120.7600 120.2930 122.0670 127.1350 109.8750
diff --git a/regtest/isdb/rt-cs2backbone/ecolvar.reference b/regtest/isdb/rt-cs2backbone/ecolvar.reference
index 3b51dc8305c99cee1ddf2eebb375a7477f395616..09014ef4247455a05fad185b9a1b444ed54232b2 100644
--- a/regtest/isdb/rt-cs2backbone/ecolvar.reference
+++ b/regtest/isdb/rt-cs2backbone/ecolvar.reference
@@ -1,2 +1,2 @@
-#! FIELDS time ens.cs.ca_1 ens.cs.ca_2 ens.cs.ca_3 ens.cs.ca_4 ens.cs.ca_5 ens.cs.ca_6 ens.cs.ca_7 ens.cs.ca_8 ens.cs.ca_9 ens.cs.ca_10 ens.cs.ca_11 ens.cs.ca_12 ens.cs.ca_13 ens.cs.ca_14 ens.cs.ca_15 ens.cs.ca_16 ens.cs.ca_17 ens.cs.ca_18 ens.cs.ca_19 ens.cs.ca_20 ens.cs.ca_21 ens.cs.ca_22 ens.cs.ca_23 ens.cs.ca_24 ens.cs.ca_25 ens.cs.ca_26 ens.cs.ca_27 ens.cs.ca_28 ens.cs.ca_29 ens.cs.ca_30 ens.cs.ca_31 ens.cs.ca_32 ens.cs.ca_33 ens.cs.ca_34 ens.cs.ca_35 ens.cs.ca_36 ens.cs.ca_37 ens.cs.ca_38 ens.cs.ca_39 ens.cs.ca_40 ens.cs.ca_41 ens.cs.ca_42 ens.cs.ca_43 ens.cs.ca_44 ens.cs.ca_45 ens.cs.ca_46 ens.cs.ca_47 ens.cs.ca_48 ens.cs.ca_49 ens.cs.ca_50 ens.cs.ca_52 ens.cs.ca_53 ens.cs.ca_54 ens.cs.ca_55 ens.cs.ca_56 ens.cs.ca_57 ens.cs.ca_58 ens.cs.ca_59 ens.cs.ca_60 ens.cs.ca_62 ens.cs.ca_63 ens.cs.ca_64 ens.cs.ca_65 ens.cs.ca_66 ens.cs.ca_67 ens.cs.ca_68 ens.cs.ca_69 ens.cs.ca_70 ens.cs.ca_71 ens.cs.ca_72 ens.cs.ca_73 ens.cs.ca_74 ens.cs.ca_75 ens.cs.ca_76 ens.cs.ca_77 ens.cs.ca_78 ens.cs.ca_79 ens.cs.ca_80 ens.cs.ca_81 ens.cs.ca_82 ens.cs.ca_83 ens.cs.ca_84 ens.cs.ca_85 ens.cs.ca_86 ens.cs.ca_87 ens.cs.ca_88 ens.cs.ca_89 ens.cs.ca_90 ens.cs.ca_91 ens.cs.ca_92 ens.cs.ca_93 ens.cs.ca_94 ens.cs.ca_95 ens.cs.ca_96 ens.cs.ca_97 ens.cs.ca_98 ens.cs.ca_99 ens.cs.ca_100 ens.cs.ca_101 ens.cs.ca_102 ens.cs.ca_103 ens.cs.ca_104 ens.cs.ca_105 ens.cs.ca_106 ens.cs.ca_107 ens.cs.ca_108 ens.cs.ca_109 ens.cs.ca_110 ens.cs.ca_111 ens.cs.ca_112 ens.cs.ca_113 ens.cs.ca_115 ens.cs.ca_116 ens.cs.ca_117 ens.cs.ca_118 ens.cs.ca_119 ens.cs.ca_120 ens.cs.ca_121 ens.cs.ca_122 ens.cs.ca_123 ens.cs.ca_124 ens.cs.ca_125 ens.cs.ca_126 ens.cs.ca_127 ens.cs.ca_128 ens.cs.ca_129 ens.cs.ca_130 ens.cs.ca_131 ens.cs.ca_132 ens.cs.ca_133 ens.cs.ca_134 ens.cs.ca_135 ens.cs.ca_136 ens.cs.ca_137 ens.cs.ca_138 ens.cs.ca_139 ens.cs.ca_140 ens.cs.ca_141 ens.cs.ca_142 ens.cs.ca_143 ens.cs.ca_144 ens.cs.ca_145 ens.cs.ca_146 ens.cs.ca_147 ens.cs.ca_148 ens.cs.ca_149 ens.cs.ca_150 ens.cs.ca_151 ens.cs.ca_152 ens.cs.ca_153 ens.cs.ca_154 ens.cs.ca_155 ens.cs.ca_156 ens.cs.ca_157 ens.cs.ca_158 ens.cs.ca_159 ens.cs.ca_161 ens.cs.ca_162 ens.cs.ca_163 ens.cs.ca_166 ens.cs.ca_171 ens.cs.ca_173 ens.cs.ca_174 ens.cs.cb_1 ens.cs.cb_2 ens.cs.cb_4 ens.cs.cb_5 ens.cs.cb_6 ens.cs.cb_7 ens.cs.cb_8 ens.cs.cb_10 ens.cs.cb_11 ens.cs.cb_12 ens.cs.cb_14 ens.cs.cb_16 ens.cs.cb_18 ens.cs.cb_19 ens.cs.cb_20 ens.cs.cb_21 ens.cs.cb_22 ens.cs.cb_23 ens.cs.cb_24 ens.cs.cb_25 ens.cs.cb_26 ens.cs.cb_27 ens.cs.cb_28 ens.cs.cb_30 ens.cs.cb_31 ens.cs.cb_32 ens.cs.cb_33 ens.cs.cb_34 ens.cs.cb_35 ens.cs.cb_36 ens.cs.cb_37 ens.cs.cb_38 ens.cs.cb_39 ens.cs.cb_40 ens.cs.cb_42 ens.cs.cb_43 ens.cs.cb_45 ens.cs.cb_47 ens.cs.cb_48 ens.cs.cb_50 ens.cs.cb_52 ens.cs.cb_54 ens.cs.cb_59 ens.cs.cb_60 ens.cs.cb_65 ens.cs.cb_66 ens.cs.cb_68 ens.cs.cb_70 ens.cs.cb_72 ens.cs.cb_75 ens.cs.cb_76 ens.cs.cb_78 ens.cs.cb_80 ens.cs.cb_81 ens.cs.cb_82 ens.cs.cb_83 ens.cs.cb_84 ens.cs.cb_85 ens.cs.cb_86 ens.cs.cb_87 ens.cs.cb_89 ens.cs.cb_90 ens.cs.cb_92 ens.cs.cb_97 ens.cs.cb_98 ens.cs.cb_99 ens.cs.cb_100 ens.cs.cb_105 ens.cs.cb_106 ens.cs.cb_107 ens.cs.cb_111 ens.cs.cb_112 ens.cs.cb_115 ens.cs.cb_116 ens.cs.cb_117 ens.cs.cb_118 ens.cs.cb_119 ens.cs.cb_120 ens.cs.cb_121 ens.cs.cb_122 ens.cs.cb_124 ens.cs.cb_126 ens.cs.cb_127 ens.cs.cb_128 ens.cs.cb_130 ens.cs.cb_131 ens.cs.cb_132 ens.cs.cb_133 ens.cs.cb_135 ens.cs.cb_136 ens.cs.cb_138 ens.cs.cb_139 ens.cs.cb_140 ens.cs.cb_141 ens.cs.cb_142 ens.cs.cb_143 ens.cs.cb_144 ens.cs.cb_146 ens.cs.cb_147 ens.cs.cb_148 ens.cs.cb_150 ens.cs.cb_151 ens.cs.cb_152 ens.cs.cb_153 ens.cs.cb_154 ens.cs.cb_156 ens.cs.cb_158 ens.cs.cb_159 ens.cs.cb_163 ens.cs.cb_166 ens.cs.cb_167 ens.cs.cb_170 ens.cs.cb_171 ens.cs.cb_173 ens.cs.hn_1 ens.cs.hn_2 ens.cs.hn_4 ens.cs.hn_5 ens.cs.hn_6 ens.cs.hn_7 ens.cs.hn_8 ens.cs.hn_9 ens.cs.hn_10 ens.cs.hn_11 ens.cs.hn_12 ens.cs.hn_13 ens.cs.hn_14 ens.cs.hn_16 ens.cs.hn_17 ens.cs.hn_18 ens.cs.hn_19 ens.cs.hn_20 ens.cs.hn_21 ens.cs.hn_22 ens.cs.hn_23 ens.cs.hn_24 ens.cs.hn_26 ens.cs.hn_27 ens.cs.hn_28 ens.cs.hn_30 ens.cs.hn_31 ens.cs.hn_32 ens.cs.hn_33 ens.cs.hn_34 ens.cs.hn_35 ens.cs.hn_36 ens.cs.hn_37 ens.cs.hn_38 ens.cs.hn_39 ens.cs.hn_40 ens.cs.hn_41 ens.cs.hn_42 ens.cs.hn_43 ens.cs.hn_44 ens.cs.hn_45 ens.cs.hn_46 ens.cs.hn_47 ens.cs.hn_48 ens.cs.hn_49 ens.cs.hn_50 ens.cs.hn_52 ens.cs.hn_53 ens.cs.hn_54 ens.cs.hn_55 ens.cs.hn_56 ens.cs.hn_58 ens.cs.hn_59 ens.cs.hn_60 ens.cs.hn_62 ens.cs.hn_63 ens.cs.hn_64 ens.cs.hn_65 ens.cs.hn_66 ens.cs.hn_67 ens.cs.hn_68 ens.cs.hn_69 ens.cs.hn_70 ens.cs.hn_71 ens.cs.hn_72 ens.cs.hn_73 ens.cs.hn_74 ens.cs.hn_75 ens.cs.hn_76 ens.cs.hn_77 ens.cs.hn_78 ens.cs.hn_79 ens.cs.hn_80 ens.cs.hn_81 ens.cs.hn_82 ens.cs.hn_83 ens.cs.hn_84 ens.cs.hn_85 ens.cs.hn_86 ens.cs.hn_87 ens.cs.hn_88 ens.cs.hn_89 ens.cs.hn_90 ens.cs.hn_91 ens.cs.hn_92 ens.cs.hn_93 ens.cs.hn_95 ens.cs.hn_96 ens.cs.hn_97 ens.cs.hn_98 ens.cs.hn_99 ens.cs.hn_102 ens.cs.hn_103 ens.cs.hn_105 ens.cs.hn_106 ens.cs.hn_107 ens.cs.hn_108 ens.cs.hn_109 ens.cs.hn_110 ens.cs.hn_111 ens.cs.hn_112 ens.cs.hn_113 ens.cs.hn_115 ens.cs.hn_116 ens.cs.hn_117 ens.cs.hn_118 ens.cs.hn_119 ens.cs.hn_120 ens.cs.hn_121 ens.cs.hn_122 ens.cs.hn_123 ens.cs.hn_124 ens.cs.hn_125 ens.cs.hn_126 ens.cs.hn_127 ens.cs.hn_128 ens.cs.hn_129 ens.cs.hn_130 ens.cs.hn_131 ens.cs.hn_132 ens.cs.hn_133 ens.cs.hn_134 ens.cs.hn_135 ens.cs.hn_136 ens.cs.hn_137 ens.cs.hn_138 ens.cs.hn_139 ens.cs.hn_140 ens.cs.hn_141 ens.cs.hn_142 ens.cs.hn_143 ens.cs.hn_144 ens.cs.hn_145 ens.cs.hn_146 ens.cs.hn_147 ens.cs.hn_148 ens.cs.hn_149 ens.cs.hn_150 ens.cs.hn_151 ens.cs.hn_152 ens.cs.hn_153 ens.cs.hn_154 ens.cs.hn_155 ens.cs.hn_156 ens.cs.hn_157 ens.cs.hn_158 ens.cs.hn_159 ens.cs.hn_161 ens.cs.hn_162 ens.cs.hn_163 ens.cs.hn_166 ens.cs.hn_170 ens.cs.hn_171 ens.cs.hn_172 ens.cs.hn_173 ens.cs.hn_174 ens.cs.nh_1 ens.cs.nh_2 ens.cs.nh_4 ens.cs.nh_5 ens.cs.nh_6 ens.cs.nh_7 ens.cs.nh_8 ens.cs.nh_9 ens.cs.nh_10 ens.cs.nh_11 ens.cs.nh_12 ens.cs.nh_13 ens.cs.nh_14 ens.cs.nh_16 ens.cs.nh_17 ens.cs.nh_18 ens.cs.nh_19 ens.cs.nh_20 ens.cs.nh_21 ens.cs.nh_22 ens.cs.nh_23 ens.cs.nh_24 ens.cs.nh_25 ens.cs.nh_26 ens.cs.nh_27 ens.cs.nh_28 ens.cs.nh_30 ens.cs.nh_31 ens.cs.nh_32 ens.cs.nh_33 ens.cs.nh_34 ens.cs.nh_35 ens.cs.nh_36 ens.cs.nh_37 ens.cs.nh_38 ens.cs.nh_39 ens.cs.nh_40 ens.cs.nh_41 ens.cs.nh_42 ens.cs.nh_43 ens.cs.nh_44 ens.cs.nh_45 ens.cs.nh_46 ens.cs.nh_47 ens.cs.nh_48 ens.cs.nh_49 ens.cs.nh_50 ens.cs.nh_52 ens.cs.nh_53 ens.cs.nh_54 ens.cs.nh_55 ens.cs.nh_56 ens.cs.nh_58 ens.cs.nh_59 ens.cs.nh_60 ens.cs.nh_62 ens.cs.nh_63 ens.cs.nh_64 ens.cs.nh_65 ens.cs.nh_66 ens.cs.nh_67 ens.cs.nh_68 ens.cs.nh_69 ens.cs.nh_70 ens.cs.nh_71 ens.cs.nh_72 ens.cs.nh_73 ens.cs.nh_74 ens.cs.nh_75 ens.cs.nh_76 ens.cs.nh_77 ens.cs.nh_78 ens.cs.nh_79 ens.cs.nh_80 ens.cs.nh_81 ens.cs.nh_82 ens.cs.nh_83 ens.cs.nh_84 ens.cs.nh_85 ens.cs.nh_86 ens.cs.nh_87 ens.cs.nh_88 ens.cs.nh_89 ens.cs.nh_90 ens.cs.nh_91 ens.cs.nh_92 ens.cs.nh_93 ens.cs.nh_95 ens.cs.nh_96 ens.cs.nh_97 ens.cs.nh_98 ens.cs.nh_99 ens.cs.nh_102 ens.cs.nh_103 ens.cs.nh_105 ens.cs.nh_106 ens.cs.nh_107 ens.cs.nh_108 ens.cs.nh_109 ens.cs.nh_110 ens.cs.nh_111 ens.cs.nh_112 ens.cs.nh_113 ens.cs.nh_115 ens.cs.nh_116 ens.cs.nh_117 ens.cs.nh_118 ens.cs.nh_119 ens.cs.nh_120 ens.cs.nh_121 ens.cs.nh_122 ens.cs.nh_123 ens.cs.nh_124 ens.cs.nh_126 ens.cs.nh_127 ens.cs.nh_128 ens.cs.nh_129 ens.cs.nh_130 ens.cs.nh_131 ens.cs.nh_132 ens.cs.nh_133 ens.cs.nh_134 ens.cs.nh_135 ens.cs.nh_136 ens.cs.nh_137 ens.cs.nh_138 ens.cs.nh_139 ens.cs.nh_140 ens.cs.nh_141 ens.cs.nh_142 ens.cs.nh_143 ens.cs.nh_144 ens.cs.nh_145 ens.cs.nh_146 ens.cs.nh_147 ens.cs.nh_148 ens.cs.nh_149 ens.cs.nh_150 ens.cs.nh_151 ens.cs.nh_152 ens.cs.nh_153 ens.cs.nh_154 ens.cs.nh_155 ens.cs.nh_156 ens.cs.nh_157 ens.cs.nh_158 ens.cs.nh_159 ens.cs.nh_161 ens.cs.nh_162 ens.cs.nh_163 ens.cs.nh_166 ens.cs.nh_170 ens.cs.nh_171 ens.cs.nh_172 ens.cs.nh_173 ens.cs.nh_174
+#! FIELDS time ens.cs.ca_2 ens.cs.ca_3 ens.cs.ca_4 ens.cs.ca_5 ens.cs.ca_6 ens.cs.ca_7 ens.cs.ca_8 ens.cs.ca_9 ens.cs.ca_10 ens.cs.ca_11 ens.cs.ca_12 ens.cs.ca_13 ens.cs.ca_14 ens.cs.ca_15 ens.cs.ca_16 ens.cs.ca_17 ens.cs.ca_18 ens.cs.ca_19 ens.cs.ca_20 ens.cs.ca_21 ens.cs.ca_22 ens.cs.ca_23 ens.cs.ca_24 ens.cs.ca_25 ens.cs.ca_26 ens.cs.ca_27 ens.cs.ca_28 ens.cs.ca_29 ens.cs.ca_30 ens.cs.ca_31 ens.cs.ca_32 ens.cs.ca_33 ens.cs.ca_34 ens.cs.ca_35 ens.cs.ca_36 ens.cs.ca_37 ens.cs.ca_38 ens.cs.ca_39 ens.cs.ca_40 ens.cs.ca_41 ens.cs.ca_42 ens.cs.ca_43 ens.cs.ca_44 ens.cs.ca_45 ens.cs.ca_46 ens.cs.ca_47 ens.cs.ca_48 ens.cs.ca_49 ens.cs.ca_50 ens.cs.ca_51 ens.cs.ca_53 ens.cs.ca_54 ens.cs.ca_55 ens.cs.ca_56 ens.cs.ca_57 ens.cs.ca_58 ens.cs.ca_59 ens.cs.ca_60 ens.cs.ca_61 ens.cs.ca_63 ens.cs.ca_64 ens.cs.ca_65 ens.cs.ca_66 ens.cs.ca_67 ens.cs.ca_68 ens.cs.ca_69 ens.cs.ca_70 ens.cs.ca_71 ens.cs.ca_72 ens.cs.ca_73 ens.cs.ca_74 ens.cs.ca_75 ens.cs.ca_76 ens.cs.ca_77 ens.cs.ca_78 ens.cs.ca_79 ens.cs.ca_80 ens.cs.ca_81 ens.cs.ca_82 ens.cs.ca_83 ens.cs.ca_84 ens.cs.ca_85 ens.cs.ca_86 ens.cs.ca_87 ens.cs.ca_88 ens.cs.ca_89 ens.cs.ca_90 ens.cs.ca_91 ens.cs.ca_92 ens.cs.ca_93 ens.cs.ca_94 ens.cs.ca_95 ens.cs.ca_96 ens.cs.ca_97 ens.cs.ca_98 ens.cs.ca_99 ens.cs.ca_100 ens.cs.ca_101 ens.cs.ca_102 ens.cs.ca_103 ens.cs.ca_104 ens.cs.ca_105 ens.cs.ca_106 ens.cs.ca_107 ens.cs.ca_108 ens.cs.ca_109 ens.cs.ca_110 ens.cs.ca_111 ens.cs.ca_112 ens.cs.ca_113 ens.cs.ca_114 ens.cs.ca_116 ens.cs.ca_117 ens.cs.ca_118 ens.cs.ca_119 ens.cs.ca_120 ens.cs.ca_121 ens.cs.ca_122 ens.cs.ca_123 ens.cs.ca_124 ens.cs.ca_125 ens.cs.ca_126 ens.cs.ca_127 ens.cs.ca_128 ens.cs.ca_129 ens.cs.ca_130 ens.cs.ca_131 ens.cs.ca_132 ens.cs.ca_133 ens.cs.ca_134 ens.cs.ca_135 ens.cs.ca_136 ens.cs.ca_137 ens.cs.ca_138 ens.cs.ca_139 ens.cs.ca_140 ens.cs.ca_141 ens.cs.ca_142 ens.cs.ca_143 ens.cs.ca_144 ens.cs.ca_145 ens.cs.ca_146 ens.cs.ca_147 ens.cs.ca_148 ens.cs.ca_149 ens.cs.ca_150 ens.cs.ca_151 ens.cs.ca_152 ens.cs.ca_153 ens.cs.ca_154 ens.cs.ca_155 ens.cs.ca_156 ens.cs.ca_157 ens.cs.ca_158 ens.cs.ca_159 ens.cs.ca_160 ens.cs.ca_162 ens.cs.ca_163 ens.cs.ca_164 ens.cs.ca_167 ens.cs.ca_172 ens.cs.ca_174 ens.cs.ca_175 ens.cs.cb_2 ens.cs.cb_3 ens.cs.cb_5 ens.cs.cb_6 ens.cs.cb_7 ens.cs.cb_8 ens.cs.cb_9 ens.cs.cb_11 ens.cs.cb_12 ens.cs.cb_13 ens.cs.cb_15 ens.cs.cb_17 ens.cs.cb_19 ens.cs.cb_20 ens.cs.cb_21 ens.cs.cb_22 ens.cs.cb_23 ens.cs.cb_24 ens.cs.cb_25 ens.cs.cb_26 ens.cs.cb_27 ens.cs.cb_28 ens.cs.cb_29 ens.cs.cb_31 ens.cs.cb_32 ens.cs.cb_33 ens.cs.cb_34 ens.cs.cb_35 ens.cs.cb_36 ens.cs.cb_37 ens.cs.cb_38 ens.cs.cb_39 ens.cs.cb_40 ens.cs.cb_41 ens.cs.cb_43 ens.cs.cb_44 ens.cs.cb_46 ens.cs.cb_48 ens.cs.cb_49 ens.cs.cb_51 ens.cs.cb_53 ens.cs.cb_55 ens.cs.cb_60 ens.cs.cb_61 ens.cs.cb_66 ens.cs.cb_67 ens.cs.cb_69 ens.cs.cb_71 ens.cs.cb_73 ens.cs.cb_76 ens.cs.cb_77 ens.cs.cb_79 ens.cs.cb_81 ens.cs.cb_82 ens.cs.cb_83 ens.cs.cb_84 ens.cs.cb_85 ens.cs.cb_86 ens.cs.cb_87 ens.cs.cb_88 ens.cs.cb_90 ens.cs.cb_91 ens.cs.cb_93 ens.cs.cb_98 ens.cs.cb_99 ens.cs.cb_100 ens.cs.cb_101 ens.cs.cb_106 ens.cs.cb_107 ens.cs.cb_108 ens.cs.cb_112 ens.cs.cb_113 ens.cs.cb_116 ens.cs.cb_117 ens.cs.cb_118 ens.cs.cb_119 ens.cs.cb_120 ens.cs.cb_121 ens.cs.cb_122 ens.cs.cb_123 ens.cs.cb_125 ens.cs.cb_127 ens.cs.cb_128 ens.cs.cb_129 ens.cs.cb_131 ens.cs.cb_132 ens.cs.cb_133 ens.cs.cb_134 ens.cs.cb_136 ens.cs.cb_137 ens.cs.cb_139 ens.cs.cb_140 ens.cs.cb_141 ens.cs.cb_142 ens.cs.cb_143 ens.cs.cb_144 ens.cs.cb_145 ens.cs.cb_147 ens.cs.cb_148 ens.cs.cb_149 ens.cs.cb_151 ens.cs.cb_152 ens.cs.cb_153 ens.cs.cb_154 ens.cs.cb_155 ens.cs.cb_157 ens.cs.cb_159 ens.cs.cb_160 ens.cs.cb_164 ens.cs.cb_167 ens.cs.cb_168 ens.cs.cb_171 ens.cs.cb_172 ens.cs.cb_174 ens.cs.hn_2 ens.cs.hn_3 ens.cs.hn_5 ens.cs.hn_6 ens.cs.hn_7 ens.cs.hn_8 ens.cs.hn_9 ens.cs.hn_10 ens.cs.hn_11 ens.cs.hn_12 ens.cs.hn_13 ens.cs.hn_14 ens.cs.hn_15 ens.cs.hn_17 ens.cs.hn_18 ens.cs.hn_19 ens.cs.hn_20 ens.cs.hn_21 ens.cs.hn_22 ens.cs.hn_23 ens.cs.hn_24 ens.cs.hn_25 ens.cs.hn_27 ens.cs.hn_28 ens.cs.hn_29 ens.cs.hn_31 ens.cs.hn_32 ens.cs.hn_33 ens.cs.hn_34 ens.cs.hn_35 ens.cs.hn_36 ens.cs.hn_37 ens.cs.hn_38 ens.cs.hn_39 ens.cs.hn_40 ens.cs.hn_41 ens.cs.hn_42 ens.cs.hn_43 ens.cs.hn_44 ens.cs.hn_45 ens.cs.hn_46 ens.cs.hn_47 ens.cs.hn_48 ens.cs.hn_49 ens.cs.hn_50 ens.cs.hn_51 ens.cs.hn_53 ens.cs.hn_54 ens.cs.hn_55 ens.cs.hn_56 ens.cs.hn_57 ens.cs.hn_59 ens.cs.hn_60 ens.cs.hn_61 ens.cs.hn_63 ens.cs.hn_64 ens.cs.hn_65 ens.cs.hn_66 ens.cs.hn_67 ens.cs.hn_68 ens.cs.hn_69 ens.cs.hn_70 ens.cs.hn_71 ens.cs.hn_72 ens.cs.hn_73 ens.cs.hn_74 ens.cs.hn_75 ens.cs.hn_76 ens.cs.hn_77 ens.cs.hn_78 ens.cs.hn_79 ens.cs.hn_80 ens.cs.hn_81 ens.cs.hn_82 ens.cs.hn_83 ens.cs.hn_84 ens.cs.hn_85 ens.cs.hn_86 ens.cs.hn_87 ens.cs.hn_88 ens.cs.hn_89 ens.cs.hn_90 ens.cs.hn_91 ens.cs.hn_92 ens.cs.hn_93 ens.cs.hn_94 ens.cs.hn_96 ens.cs.hn_97 ens.cs.hn_98 ens.cs.hn_99 ens.cs.hn_100 ens.cs.hn_103 ens.cs.hn_104 ens.cs.hn_106 ens.cs.hn_107 ens.cs.hn_108 ens.cs.hn_109 ens.cs.hn_110 ens.cs.hn_111 ens.cs.hn_112 ens.cs.hn_113 ens.cs.hn_114 ens.cs.hn_116 ens.cs.hn_117 ens.cs.hn_118 ens.cs.hn_119 ens.cs.hn_120 ens.cs.hn_121 ens.cs.hn_122 ens.cs.hn_123 ens.cs.hn_124 ens.cs.hn_125 ens.cs.hn_126 ens.cs.hn_127 ens.cs.hn_128 ens.cs.hn_129 ens.cs.hn_130 ens.cs.hn_131 ens.cs.hn_132 ens.cs.hn_133 ens.cs.hn_134 ens.cs.hn_135 ens.cs.hn_136 ens.cs.hn_137 ens.cs.hn_138 ens.cs.hn_139 ens.cs.hn_140 ens.cs.hn_141 ens.cs.hn_142 ens.cs.hn_143 ens.cs.hn_144 ens.cs.hn_145 ens.cs.hn_146 ens.cs.hn_147 ens.cs.hn_148 ens.cs.hn_149 ens.cs.hn_150 ens.cs.hn_151 ens.cs.hn_152 ens.cs.hn_153 ens.cs.hn_154 ens.cs.hn_155 ens.cs.hn_156 ens.cs.hn_157 ens.cs.hn_158 ens.cs.hn_159 ens.cs.hn_160 ens.cs.hn_162 ens.cs.hn_163 ens.cs.hn_164 ens.cs.hn_167 ens.cs.hn_171 ens.cs.hn_172 ens.cs.hn_173 ens.cs.hn_174 ens.cs.hn_175 ens.cs.nh_2 ens.cs.nh_3 ens.cs.nh_5 ens.cs.nh_6 ens.cs.nh_7 ens.cs.nh_8 ens.cs.nh_9 ens.cs.nh_10 ens.cs.nh_11 ens.cs.nh_12 ens.cs.nh_13 ens.cs.nh_14 ens.cs.nh_15 ens.cs.nh_17 ens.cs.nh_18 ens.cs.nh_19 ens.cs.nh_20 ens.cs.nh_21 ens.cs.nh_22 ens.cs.nh_23 ens.cs.nh_24 ens.cs.nh_25 ens.cs.nh_26 ens.cs.nh_27 ens.cs.nh_28 ens.cs.nh_29 ens.cs.nh_31 ens.cs.nh_32 ens.cs.nh_33 ens.cs.nh_34 ens.cs.nh_35 ens.cs.nh_36 ens.cs.nh_37 ens.cs.nh_38 ens.cs.nh_39 ens.cs.nh_40 ens.cs.nh_41 ens.cs.nh_42 ens.cs.nh_43 ens.cs.nh_44 ens.cs.nh_45 ens.cs.nh_46 ens.cs.nh_47 ens.cs.nh_48 ens.cs.nh_49 ens.cs.nh_50 ens.cs.nh_51 ens.cs.nh_53 ens.cs.nh_54 ens.cs.nh_55 ens.cs.nh_56 ens.cs.nh_57 ens.cs.nh_59 ens.cs.nh_60 ens.cs.nh_61 ens.cs.nh_63 ens.cs.nh_64 ens.cs.nh_65 ens.cs.nh_66 ens.cs.nh_67 ens.cs.nh_68 ens.cs.nh_69 ens.cs.nh_70 ens.cs.nh_71 ens.cs.nh_72 ens.cs.nh_73 ens.cs.nh_74 ens.cs.nh_75 ens.cs.nh_76 ens.cs.nh_77 ens.cs.nh_78 ens.cs.nh_79 ens.cs.nh_80 ens.cs.nh_81 ens.cs.nh_82 ens.cs.nh_83 ens.cs.nh_84 ens.cs.nh_85 ens.cs.nh_86 ens.cs.nh_87 ens.cs.nh_88 ens.cs.nh_89 ens.cs.nh_90 ens.cs.nh_91 ens.cs.nh_92 ens.cs.nh_93 ens.cs.nh_94 ens.cs.nh_96 ens.cs.nh_97 ens.cs.nh_98 ens.cs.nh_99 ens.cs.nh_100 ens.cs.nh_103 ens.cs.nh_104 ens.cs.nh_106 ens.cs.nh_107 ens.cs.nh_108 ens.cs.nh_109 ens.cs.nh_110 ens.cs.nh_111 ens.cs.nh_112 ens.cs.nh_113 ens.cs.nh_114 ens.cs.nh_116 ens.cs.nh_117 ens.cs.nh_118 ens.cs.nh_119 ens.cs.nh_120 ens.cs.nh_121 ens.cs.nh_122 ens.cs.nh_123 ens.cs.nh_124 ens.cs.nh_125 ens.cs.nh_127 ens.cs.nh_128 ens.cs.nh_129 ens.cs.nh_130 ens.cs.nh_131 ens.cs.nh_132 ens.cs.nh_133 ens.cs.nh_134 ens.cs.nh_135 ens.cs.nh_136 ens.cs.nh_137 ens.cs.nh_138 ens.cs.nh_139 ens.cs.nh_140 ens.cs.nh_141 ens.cs.nh_142 ens.cs.nh_143 ens.cs.nh_144 ens.cs.nh_145 ens.cs.nh_146 ens.cs.nh_147 ens.cs.nh_148 ens.cs.nh_149 ens.cs.nh_150 ens.cs.nh_151 ens.cs.nh_152 ens.cs.nh_153 ens.cs.nh_154 ens.cs.nh_155 ens.cs.nh_156 ens.cs.nh_157 ens.cs.nh_158 ens.cs.nh_159 ens.cs.nh_160 ens.cs.nh_162 ens.cs.nh_163 ens.cs.nh_164 ens.cs.nh_167 ens.cs.nh_171 ens.cs.nh_172 ens.cs.nh_173 ens.cs.nh_174 ens.cs.nh_175
0.000000 62.0730 52.3706 64.4137 59.7863 60.6879 56.4595 56.0189 54.5454 59.4599 51.2394 61.2660 54.6233 44.3991 53.6047 62.8787 55.2518 44.2747 54.7131 60.9540 55.9041 56.8460 55.1113 53.3852 57.3596 52.2858 55.6175 57.6336 53.6239 64.1857 59.1132 66.8493 55.7794 59.1292 55.0374 60.1025 58.8113 53.1038 56.0572 62.2068 63.4757 45.1819 59.3763 56.6704 44.5722 54.6029 44.9747 56.6078 59.5705 45.0354 60.4493 58.9363 47.1741 55.0026 59.9832 60.2715 62.1029 45.2073 57.6760 53.4603 55.3549 42.8546 42.5432 54.1798 54.6084 62.7618 55.5677 46.0571 52.5093 44.6140 62.5575 46.5935 45.1526 55.6616 56.6487 61.8745 55.7714 42.8489 59.9596 53.4024 54.6861 55.3909 56.1854 57.8877 52.5591 57.1525 64.5239 52.4386 54.6889 47.4524 62.0905 44.6840 62.0626 47.0500 59.8543 53.0972 56.3258 52.8093 53.3313 51.0327 50.5406 42.9156 62.4402 54.7643 59.5677 53.4653 44.6307 56.9849 57.1094 56.4790 54.5636 58.8532 60.8029 50.6872 58.2398 58.9570 59.6962 62.1340 56.3216 55.7682 45.6923 54.5934 46.7144 61.6256 62.6774 57.4535 44.6239 54.1576 63.4026 57.6458 54.4580 45.2629 58.4273 55.3277 62.9301 65.4181 59.9661 53.9957 57.6088 57.9670 57.9326 57.2349 43.3458 55.5668 60.0078 54.7210 44.1874 56.3149 59.1342 57.8373 53.6586 56.1674 60.7704 59.6696 60.7819 51.6383 51.7341 44.0541 55.4662 53.8065 56.7795 54.2547 53.5108 42.7161 34.2937 38.9559 71.7660 34.8127 42.2615 42.6553 39.8590 21.4642 34.0789 38.3226 31.2951 43.6700 32.1148 34.0880 65.4524 42.6126 32.8132 43.4997 37.4657 18.2169 39.0673 33.9617 42.3412 31.5770 68.1900 18.4224 29.1037 37.8974 39.6410 30.5450 18.7755 41.6034 63.1973 68.7844 29.3334 30.2885 40.9613 39.1245 30.4924 64.2948 35.9660 32.1716 41.9359 33.7734 39.1255 38.6119 31.7084 39.5749 69.6243 35.1265 65.8722 37.9460 29.6275 36.1351 42.1447 30.7567 40.4355 31.0297 42.1361 40.1515 42.9276 35.9857 71.0150 43.1114 65.8322 32.5373 18.9061 36.3863 69.8383 38.8008 43.1785 42.1500 69.1031 21.0233 32.4623 68.9980 29.7404 28.1435 40.7358 40.0967 35.0409 34.0597 31.3908 42.0009 35.3772 31.6183 33.6728 32.0497 31.2342 38.1085 31.1480 29.1712 18.3978 32.6398 29.8797 29.9299 38.5390 66.6853 28.9447 38.8034 31.8682 69.4484 63.3771 35.8460 32.2684 71.7774 19.5422 44.0455 45.3084 65.5408 39.6278 44.2547 41.4515 19.3336 8.3956 8.1848 8.6158 8.4258 8.4709 9.3888 9.4444 9.3433 9.2101 8.5786 9.3666 7.9867 7.6985 9.1791 7.8827 8.2093 8.8014 8.1572 9.2300 9.0427 8.5182 8.8400 8.2006 7.7422 8.0822 8.9440 9.5478 8.2073 7.6799 8.0440 7.6348 8.4802 8.0264 7.6663 7.9577 7.5794 7.4226 7.9847 8.1008 7.6811 6.8613 8.2277 8.0954 7.8048 9.0453 8.6393 8.9681 7.9238 7.6758 9.1173 9.0910 9.7445 8.3904 8.2988 9.4149 8.3619 8.2689 9.6085 7.4959 7.7449 8.4161 8.0767 7.9356 9.1390 8.1650 8.4150 8.3073 6.5523 8.3250 8.6975 7.7499 7.5113 8.9392 7.9568 8.5391 9.4452 8.7498 9.0756 7.9118 8.1422 7.5522 8.3382 8.5531 9.7142 8.2704 8.0184 9.4378 7.4284 8.0328 8.1573 8.7344 8.7015 7.7948 9.4030 8.4866 7.5671 8.4926 8.5786 8.1205 8.5526 9.1677 8.8688 8.9762 8.0568 8.4637 8.3728 8.3783 8.0683 7.4686 7.9969 8.9155 7.6074 8.5530 8.2950 8.5958 8.8931 7.1535 8.7365 9.2700 8.7580 7.9432 8.7734 8.1949 8.1992 7.7894 7.8197 8.0927 7.7994 7.5572 8.2136 7.7122 8.0369 7.5493 8.5914 8.7952 8.1163 8.3927 8.0338 8.6052 9.2808 7.7869 8.6136 8.8987 8.5515 8.4698 8.8166 8.1780 6.4731 8.4875 8.5228 8.2109 8.9355 8.5985 7.0547 8.0462 8.3482 116.6918 121.9062 114.8220 119.9097 121.5690 121.6931 130.2132 125.6208 130.5275 122.4980 126.2708 109.6879 120.4056 126.1067 106.7693 122.4414 121.7389 118.0299 121.7100 124.5624 124.7386 122.5234 126.5566 119.2430 118.2675 120.1204 120.3851 120.9825 121.9306 120.6263 117.5530 119.4497 116.7107 119.1598 119.0635 116.5841 107.6017 109.7018 121.1796 119.2702 109.3037 112.2750 103.9334 115.7907 126.7110 115.9154 120.1176 125.7704 114.6887 122.0560 125.3974 129.2830 112.5522 120.4731 115.2584 126.9208 109.2336 109.7778 123.1069 117.5301 111.6849 119.2762 109.9256 113.6238 107.2713 110.6054 113.5356 113.1287 121.9717 115.4850 113.4984 115.5951 107.4014 123.0122 114.1364 117.5227 118.8666 123.1010 126.3742 117.0101 117.7327 123.3504 121.2959 121.6423 115.4650 109.2847 111.8720 112.0057 118.4960 125.8575 120.0978 123.2555 121.4647 110.8560 121.4479 113.0550 121.9223 110.3643 113.8355 123.4550 122.0488 117.4141 119.6662 116.4161 122.5649 125.3708 114.8163 126.9575 115.9813 120.4407 124.5692 111.9737 118.9638 121.5864 128.5934 121.6842 106.8831 121.7053 125.4221 128.3906 117.8737 111.0562 119.3753 116.2936 118.4522 122.6199 119.6260 121.3386 117.0253 114.4167 116.4174 116.7625 104.7602 113.5643 124.0201 117.2104 109.6820 122.4872 115.3610 116.3335 118.3537 122.7614 129.0059 117.9062 122.6280 126.7315 113.0731 107.3245 125.3253 123.5263 115.4587 120.3210 117.9950 114.7509 124.4085 107.8531
diff --git a/regtest/isdb/rt-cs2backbone/forces.reference b/regtest/isdb/rt-cs2backbone/forces.reference
index 550978b5fb0d45b31805ad2449260ae8bc8395d6..83844ae1b4aa78314b3c1bd18625658e16b38933 100644
--- a/regtest/isdb/rt-cs2backbone/forces.reference
+++ b/regtest/isdb/rt-cs2backbone/forces.reference
@@ -1,2 +1,2 @@
-#! FIELDS time cs.ca_1 cs.ca_2 cs.ca_3 cs.ca_4 cs.ca_5 cs.ca_6 cs.ca_7 cs.ca_8 cs.ca_9 cs.ca_10 cs.ca_11 cs.ca_12 cs.ca_13 cs.ca_14 cs.ca_15 cs.ca_16 cs.ca_17 cs.ca_18 cs.ca_19 cs.ca_20 cs.ca_21 cs.ca_22 cs.ca_23 cs.ca_24 cs.ca_25 cs.ca_26 cs.ca_27 cs.ca_28 cs.ca_29 cs.ca_30 cs.ca_31 cs.ca_32 cs.ca_33 cs.ca_34 cs.ca_35 cs.ca_36 cs.ca_37 cs.ca_38 cs.ca_39 cs.ca_40 cs.ca_41 cs.ca_42 cs.ca_43 cs.ca_44 cs.ca_45 cs.ca_46 cs.ca_47 cs.ca_48 cs.ca_49 cs.ca_50 cs.ca_52 cs.ca_53 cs.ca_54 cs.ca_55 cs.ca_56 cs.ca_57 cs.ca_58 cs.ca_59 cs.ca_60 cs.ca_62 cs.ca_63 cs.ca_64 cs.ca_65 cs.ca_66 cs.ca_67 cs.ca_68 cs.ca_69 cs.ca_70 cs.ca_71 cs.ca_72 cs.ca_73 cs.ca_74 cs.ca_75 cs.ca_76 cs.ca_77 cs.ca_78 cs.ca_79 cs.ca_80 cs.ca_81 cs.ca_82 cs.ca_83 cs.ca_84 cs.ca_85 cs.ca_86 cs.ca_87 cs.ca_88 cs.ca_89 cs.ca_90 cs.ca_91 cs.ca_92 cs.ca_93 cs.ca_94 cs.ca_95 cs.ca_96 cs.ca_97 cs.ca_98 cs.ca_99 cs.ca_100 cs.ca_101 cs.ca_102 cs.ca_103 cs.ca_104 cs.ca_105 cs.ca_106 cs.ca_107 cs.ca_108 cs.ca_109 cs.ca_110 cs.ca_111 cs.ca_112 cs.ca_113 cs.ca_115 cs.ca_116 cs.ca_117 cs.ca_118 cs.ca_119 cs.ca_120 cs.ca_121 cs.ca_122 cs.ca_123 cs.ca_124 cs.ca_125 cs.ca_126 cs.ca_127 cs.ca_128 cs.ca_129 cs.ca_130 cs.ca_131 cs.ca_132 cs.ca_133 cs.ca_134 cs.ca_135 cs.ca_136 cs.ca_137 cs.ca_138 cs.ca_139 cs.ca_140 cs.ca_141 cs.ca_142 cs.ca_143 cs.ca_144 cs.ca_145 cs.ca_146 cs.ca_147 cs.ca_148 cs.ca_149 cs.ca_150 cs.ca_151 cs.ca_152 cs.ca_153 cs.ca_154 cs.ca_155 cs.ca_156 cs.ca_157 cs.ca_158 cs.ca_159 cs.ca_161 cs.ca_162 cs.ca_163 cs.ca_166 cs.ca_171 cs.ca_173 cs.ca_174 cs.cb_1 cs.cb_2 cs.cb_4 cs.cb_5 cs.cb_6 cs.cb_7 cs.cb_8 cs.cb_10 cs.cb_11 cs.cb_12 cs.cb_14 cs.cb_16 cs.cb_18 cs.cb_19 cs.cb_20 cs.cb_21 cs.cb_22 cs.cb_23 cs.cb_24 cs.cb_25 cs.cb_26 cs.cb_27 cs.cb_28 cs.cb_30 cs.cb_31 cs.cb_32 cs.cb_33 cs.cb_34 cs.cb_35 cs.cb_36 cs.cb_37 cs.cb_38 cs.cb_39 cs.cb_40 cs.cb_42 cs.cb_43 cs.cb_45 cs.cb_47 cs.cb_48 cs.cb_50 cs.cb_52 cs.cb_54 cs.cb_59 cs.cb_60 cs.cb_65 cs.cb_66 cs.cb_68 cs.cb_70 cs.cb_72 cs.cb_75 cs.cb_76 cs.cb_78 cs.cb_80 cs.cb_81 cs.cb_82 cs.cb_83 cs.cb_84 cs.cb_85 cs.cb_86 cs.cb_87 cs.cb_89 cs.cb_90 cs.cb_92 cs.cb_97 cs.cb_98 cs.cb_99 cs.cb_100 cs.cb_105 cs.cb_106 cs.cb_107 cs.cb_111 cs.cb_112 cs.cb_115 cs.cb_116 cs.cb_117 cs.cb_118 cs.cb_119 cs.cb_120 cs.cb_121 cs.cb_122 cs.cb_124 cs.cb_126 cs.cb_127 cs.cb_128 cs.cb_130 cs.cb_131 cs.cb_132 cs.cb_133 cs.cb_135 cs.cb_136 cs.cb_138 cs.cb_139 cs.cb_140 cs.cb_141 cs.cb_142 cs.cb_143 cs.cb_144 cs.cb_146 cs.cb_147 cs.cb_148 cs.cb_150 cs.cb_151 cs.cb_152 cs.cb_153 cs.cb_154 cs.cb_156 cs.cb_158 cs.cb_159 cs.cb_163 cs.cb_166 cs.cb_167 cs.cb_170 cs.cb_171 cs.cb_173 cs.hn_1 cs.hn_2 cs.hn_4 cs.hn_5 cs.hn_6 cs.hn_7 cs.hn_8 cs.hn_9 cs.hn_10 cs.hn_11 cs.hn_12 cs.hn_13 cs.hn_14 cs.hn_16 cs.hn_17 cs.hn_18 cs.hn_19 cs.hn_20 cs.hn_21 cs.hn_22 cs.hn_23 cs.hn_24 cs.hn_26 cs.hn_27 cs.hn_28 cs.hn_30 cs.hn_31 cs.hn_32 cs.hn_33 cs.hn_34 cs.hn_35 cs.hn_36 cs.hn_37 cs.hn_38 cs.hn_39 cs.hn_40 cs.hn_41 cs.hn_42 cs.hn_43 cs.hn_44 cs.hn_45 cs.hn_46 cs.hn_47 cs.hn_48 cs.hn_49 cs.hn_50 cs.hn_52 cs.hn_53 cs.hn_54 cs.hn_55 cs.hn_56 cs.hn_58 cs.hn_59 cs.hn_60 cs.hn_62 cs.hn_63 cs.hn_64 cs.hn_65 cs.hn_66 cs.hn_67 cs.hn_68 cs.hn_69 cs.hn_70 cs.hn_71 cs.hn_72 cs.hn_73 cs.hn_74 cs.hn_75 cs.hn_76 cs.hn_77 cs.hn_78 cs.hn_79 cs.hn_80 cs.hn_81 cs.hn_82 cs.hn_83 cs.hn_84 cs.hn_85 cs.hn_86 cs.hn_87 cs.hn_88 cs.hn_89 cs.hn_90 cs.hn_91 cs.hn_92 cs.hn_93 cs.hn_95 cs.hn_96 cs.hn_97 cs.hn_98 cs.hn_99 cs.hn_102 cs.hn_103 cs.hn_105 cs.hn_106 cs.hn_107 cs.hn_108 cs.hn_109 cs.hn_110 cs.hn_111 cs.hn_112 cs.hn_113 cs.hn_115 cs.hn_116 cs.hn_117 cs.hn_118 cs.hn_119 cs.hn_120 cs.hn_121 cs.hn_122 cs.hn_123 cs.hn_124 cs.hn_125 cs.hn_126 cs.hn_127 cs.hn_128 cs.hn_129 cs.hn_130 cs.hn_131 cs.hn_132 cs.hn_133 cs.hn_134 cs.hn_135 cs.hn_136 cs.hn_137 cs.hn_138 cs.hn_139 cs.hn_140 cs.hn_141 cs.hn_142 cs.hn_143 cs.hn_144 cs.hn_145 cs.hn_146 cs.hn_147 cs.hn_148 cs.hn_149 cs.hn_150 cs.hn_151 cs.hn_152 cs.hn_153 cs.hn_154 cs.hn_155 cs.hn_156 cs.hn_157 cs.hn_158 cs.hn_159 cs.hn_161 cs.hn_162 cs.hn_163 cs.hn_166 cs.hn_170 cs.hn_171 cs.hn_172 cs.hn_173 cs.hn_174 cs.nh_1 cs.nh_2 cs.nh_4 cs.nh_5 cs.nh_6 cs.nh_7 cs.nh_8 cs.nh_9 cs.nh_10 cs.nh_11 cs.nh_12 cs.nh_13 cs.nh_14 cs.nh_16 cs.nh_17 cs.nh_18 cs.nh_19 cs.nh_20 cs.nh_21 cs.nh_22 cs.nh_23 cs.nh_24 cs.nh_25 cs.nh_26 cs.nh_27 cs.nh_28 cs.nh_30 cs.nh_31 cs.nh_32 cs.nh_33 cs.nh_34 cs.nh_35 cs.nh_36 cs.nh_37 cs.nh_38 cs.nh_39 cs.nh_40 cs.nh_41 cs.nh_42 cs.nh_43 cs.nh_44 cs.nh_45 cs.nh_46 cs.nh_47 cs.nh_48 cs.nh_49 cs.nh_50 cs.nh_52 cs.nh_53 cs.nh_54 cs.nh_55 cs.nh_56 cs.nh_58 cs.nh_59 cs.nh_60 cs.nh_62 cs.nh_63 cs.nh_64 cs.nh_65 cs.nh_66 cs.nh_67 cs.nh_68 cs.nh_69 cs.nh_70 cs.nh_71 cs.nh_72 cs.nh_73 cs.nh_74 cs.nh_75 cs.nh_76 cs.nh_77 cs.nh_78 cs.nh_79 cs.nh_80 cs.nh_81 cs.nh_82 cs.nh_83 cs.nh_84 cs.nh_85 cs.nh_86 cs.nh_87 cs.nh_88 cs.nh_89 cs.nh_90 cs.nh_91 cs.nh_92 cs.nh_93 cs.nh_95 cs.nh_96 cs.nh_97 cs.nh_98 cs.nh_99 cs.nh_102 cs.nh_103 cs.nh_105 cs.nh_106 cs.nh_107 cs.nh_108 cs.nh_109 cs.nh_110 cs.nh_111 cs.nh_112 cs.nh_113 cs.nh_115 cs.nh_116 cs.nh_117 cs.nh_118 cs.nh_119 cs.nh_120 cs.nh_121 cs.nh_122 cs.nh_123 cs.nh_124 cs.nh_126 cs.nh_127 cs.nh_128 cs.nh_129 cs.nh_130 cs.nh_131 cs.nh_132 cs.nh_133 cs.nh_134 cs.nh_135 cs.nh_136 cs.nh_137 cs.nh_138 cs.nh_139 cs.nh_140 cs.nh_141 cs.nh_142 cs.nh_143 cs.nh_144 cs.nh_145 cs.nh_146 cs.nh_147 cs.nh_148 cs.nh_149 cs.nh_150 cs.nh_151 cs.nh_152 cs.nh_153 cs.nh_154 cs.nh_155 cs.nh_156 cs.nh_157 cs.nh_158 cs.nh_159 cs.nh_161 cs.nh_162 cs.nh_163 cs.nh_166 cs.nh_170 cs.nh_171 cs.nh_172 cs.nh_173 cs.nh_174
+#! FIELDS time cs.ca_2 cs.ca_3 cs.ca_4 cs.ca_5 cs.ca_6 cs.ca_7 cs.ca_8 cs.ca_9 cs.ca_10 cs.ca_11 cs.ca_12 cs.ca_13 cs.ca_14 cs.ca_15 cs.ca_16 cs.ca_17 cs.ca_18 cs.ca_19 cs.ca_20 cs.ca_21 cs.ca_22 cs.ca_23 cs.ca_24 cs.ca_25 cs.ca_26 cs.ca_27 cs.ca_28 cs.ca_29 cs.ca_30 cs.ca_31 cs.ca_32 cs.ca_33 cs.ca_34 cs.ca_35 cs.ca_36 cs.ca_37 cs.ca_38 cs.ca_39 cs.ca_40 cs.ca_41 cs.ca_42 cs.ca_43 cs.ca_44 cs.ca_45 cs.ca_46 cs.ca_47 cs.ca_48 cs.ca_49 cs.ca_50 cs.ca_51 cs.ca_53 cs.ca_54 cs.ca_55 cs.ca_56 cs.ca_57 cs.ca_58 cs.ca_59 cs.ca_60 cs.ca_61 cs.ca_63 cs.ca_64 cs.ca_65 cs.ca_66 cs.ca_67 cs.ca_68 cs.ca_69 cs.ca_70 cs.ca_71 cs.ca_72 cs.ca_73 cs.ca_74 cs.ca_75 cs.ca_76 cs.ca_77 cs.ca_78 cs.ca_79 cs.ca_80 cs.ca_81 cs.ca_82 cs.ca_83 cs.ca_84 cs.ca_85 cs.ca_86 cs.ca_87 cs.ca_88 cs.ca_89 cs.ca_90 cs.ca_91 cs.ca_92 cs.ca_93 cs.ca_94 cs.ca_95 cs.ca_96 cs.ca_97 cs.ca_98 cs.ca_99 cs.ca_100 cs.ca_101 cs.ca_102 cs.ca_103 cs.ca_104 cs.ca_105 cs.ca_106 cs.ca_107 cs.ca_108 cs.ca_109 cs.ca_110 cs.ca_111 cs.ca_112 cs.ca_113 cs.ca_114 cs.ca_116 cs.ca_117 cs.ca_118 cs.ca_119 cs.ca_120 cs.ca_121 cs.ca_122 cs.ca_123 cs.ca_124 cs.ca_125 cs.ca_126 cs.ca_127 cs.ca_128 cs.ca_129 cs.ca_130 cs.ca_131 cs.ca_132 cs.ca_133 cs.ca_134 cs.ca_135 cs.ca_136 cs.ca_137 cs.ca_138 cs.ca_139 cs.ca_140 cs.ca_141 cs.ca_142 cs.ca_143 cs.ca_144 cs.ca_145 cs.ca_146 cs.ca_147 cs.ca_148 cs.ca_149 cs.ca_150 cs.ca_151 cs.ca_152 cs.ca_153 cs.ca_154 cs.ca_155 cs.ca_156 cs.ca_157 cs.ca_158 cs.ca_159 cs.ca_160 cs.ca_162 cs.ca_163 cs.ca_164 cs.ca_167 cs.ca_172 cs.ca_174 cs.ca_175 cs.cb_2 cs.cb_3 cs.cb_5 cs.cb_6 cs.cb_7 cs.cb_8 cs.cb_9 cs.cb_11 cs.cb_12 cs.cb_13 cs.cb_15 cs.cb_17 cs.cb_19 cs.cb_20 cs.cb_21 cs.cb_22 cs.cb_23 cs.cb_24 cs.cb_25 cs.cb_26 cs.cb_27 cs.cb_28 cs.cb_29 cs.cb_31 cs.cb_32 cs.cb_33 cs.cb_34 cs.cb_35 cs.cb_36 cs.cb_37 cs.cb_38 cs.cb_39 cs.cb_40 cs.cb_41 cs.cb_43 cs.cb_44 cs.cb_46 cs.cb_48 cs.cb_49 cs.cb_51 cs.cb_53 cs.cb_55 cs.cb_60 cs.cb_61 cs.cb_66 cs.cb_67 cs.cb_69 cs.cb_71 cs.cb_73 cs.cb_76 cs.cb_77 cs.cb_79 cs.cb_81 cs.cb_82 cs.cb_83 cs.cb_84 cs.cb_85 cs.cb_86 cs.cb_87 cs.cb_88 cs.cb_90 cs.cb_91 cs.cb_93 cs.cb_98 cs.cb_99 cs.cb_100 cs.cb_101 cs.cb_106 cs.cb_107 cs.cb_108 cs.cb_112 cs.cb_113 cs.cb_116 cs.cb_117 cs.cb_118 cs.cb_119 cs.cb_120 cs.cb_121 cs.cb_122 cs.cb_123 cs.cb_125 cs.cb_127 cs.cb_128 cs.cb_129 cs.cb_131 cs.cb_132 cs.cb_133 cs.cb_134 cs.cb_136 cs.cb_137 cs.cb_139 cs.cb_140 cs.cb_141 cs.cb_142 cs.cb_143 cs.cb_144 cs.cb_145 cs.cb_147 cs.cb_148 cs.cb_149 cs.cb_151 cs.cb_152 cs.cb_153 cs.cb_154 cs.cb_155 cs.cb_157 cs.cb_159 cs.cb_160 cs.cb_164 cs.cb_167 cs.cb_168 cs.cb_171 cs.cb_172 cs.cb_174 cs.hn_2 cs.hn_3 cs.hn_5 cs.hn_6 cs.hn_7 cs.hn_8 cs.hn_9 cs.hn_10 cs.hn_11 cs.hn_12 cs.hn_13 cs.hn_14 cs.hn_15 cs.hn_17 cs.hn_18 cs.hn_19 cs.hn_20 cs.hn_21 cs.hn_22 cs.hn_23 cs.hn_24 cs.hn_25 cs.hn_27 cs.hn_28 cs.hn_29 cs.hn_31 cs.hn_32 cs.hn_33 cs.hn_34 cs.hn_35 cs.hn_36 cs.hn_37 cs.hn_38 cs.hn_39 cs.hn_40 cs.hn_41 cs.hn_42 cs.hn_43 cs.hn_44 cs.hn_45 cs.hn_46 cs.hn_47 cs.hn_48 cs.hn_49 cs.hn_50 cs.hn_51 cs.hn_53 cs.hn_54 cs.hn_55 cs.hn_56 cs.hn_57 cs.hn_59 cs.hn_60 cs.hn_61 cs.hn_63 cs.hn_64 cs.hn_65 cs.hn_66 cs.hn_67 cs.hn_68 cs.hn_69 cs.hn_70 cs.hn_71 cs.hn_72 cs.hn_73 cs.hn_74 cs.hn_75 cs.hn_76 cs.hn_77 cs.hn_78 cs.hn_79 cs.hn_80 cs.hn_81 cs.hn_82 cs.hn_83 cs.hn_84 cs.hn_85 cs.hn_86 cs.hn_87 cs.hn_88 cs.hn_89 cs.hn_90 cs.hn_91 cs.hn_92 cs.hn_93 cs.hn_94 cs.hn_96 cs.hn_97 cs.hn_98 cs.hn_99 cs.hn_100 cs.hn_103 cs.hn_104 cs.hn_106 cs.hn_107 cs.hn_108 cs.hn_109 cs.hn_110 cs.hn_111 cs.hn_112 cs.hn_113 cs.hn_114 cs.hn_116 cs.hn_117 cs.hn_118 cs.hn_119 cs.hn_120 cs.hn_121 cs.hn_122 cs.hn_123 cs.hn_124 cs.hn_125 cs.hn_126 cs.hn_127 cs.hn_128 cs.hn_129 cs.hn_130 cs.hn_131 cs.hn_132 cs.hn_133 cs.hn_134 cs.hn_135 cs.hn_136 cs.hn_137 cs.hn_138 cs.hn_139 cs.hn_140 cs.hn_141 cs.hn_142 cs.hn_143 cs.hn_144 cs.hn_145 cs.hn_146 cs.hn_147 cs.hn_148 cs.hn_149 cs.hn_150 cs.hn_151 cs.hn_152 cs.hn_153 cs.hn_154 cs.hn_155 cs.hn_156 cs.hn_157 cs.hn_158 cs.hn_159 cs.hn_160 cs.hn_162 cs.hn_163 cs.hn_164 cs.hn_167 cs.hn_171 cs.hn_172 cs.hn_173 cs.hn_174 cs.hn_175 cs.nh_2 cs.nh_3 cs.nh_5 cs.nh_6 cs.nh_7 cs.nh_8 cs.nh_9 cs.nh_10 cs.nh_11 cs.nh_12 cs.nh_13 cs.nh_14 cs.nh_15 cs.nh_17 cs.nh_18 cs.nh_19 cs.nh_20 cs.nh_21 cs.nh_22 cs.nh_23 cs.nh_24 cs.nh_25 cs.nh_26 cs.nh_27 cs.nh_28 cs.nh_29 cs.nh_31 cs.nh_32 cs.nh_33 cs.nh_34 cs.nh_35 cs.nh_36 cs.nh_37 cs.nh_38 cs.nh_39 cs.nh_40 cs.nh_41 cs.nh_42 cs.nh_43 cs.nh_44 cs.nh_45 cs.nh_46 cs.nh_47 cs.nh_48 cs.nh_49 cs.nh_50 cs.nh_51 cs.nh_53 cs.nh_54 cs.nh_55 cs.nh_56 cs.nh_57 cs.nh_59 cs.nh_60 cs.nh_61 cs.nh_63 cs.nh_64 cs.nh_65 cs.nh_66 cs.nh_67 cs.nh_68 cs.nh_69 cs.nh_70 cs.nh_71 cs.nh_72 cs.nh_73 cs.nh_74 cs.nh_75 cs.nh_76 cs.nh_77 cs.nh_78 cs.nh_79 cs.nh_80 cs.nh_81 cs.nh_82 cs.nh_83 cs.nh_84 cs.nh_85 cs.nh_86 cs.nh_87 cs.nh_88 cs.nh_89 cs.nh_90 cs.nh_91 cs.nh_92 cs.nh_93 cs.nh_94 cs.nh_96 cs.nh_97 cs.nh_98 cs.nh_99 cs.nh_100 cs.nh_103 cs.nh_104 cs.nh_106 cs.nh_107 cs.nh_108 cs.nh_109 cs.nh_110 cs.nh_111 cs.nh_112 cs.nh_113 cs.nh_114 cs.nh_116 cs.nh_117 cs.nh_118 cs.nh_119 cs.nh_120 cs.nh_121 cs.nh_122 cs.nh_123 cs.nh_124 cs.nh_125 cs.nh_127 cs.nh_128 cs.nh_129 cs.nh_130 cs.nh_131 cs.nh_132 cs.nh_133 cs.nh_134 cs.nh_135 cs.nh_136 cs.nh_137 cs.nh_138 cs.nh_139 cs.nh_140 cs.nh_141 cs.nh_142 cs.nh_143 cs.nh_144 cs.nh_145 cs.nh_146 cs.nh_147 cs.nh_148 cs.nh_149 cs.nh_150 cs.nh_151 cs.nh_152 cs.nh_153 cs.nh_154 cs.nh_155 cs.nh_156 cs.nh_157 cs.nh_158 cs.nh_159 cs.nh_160 cs.nh_162 cs.nh_163 cs.nh_164 cs.nh_167 cs.nh_171 cs.nh_172 cs.nh_173 cs.nh_174 cs.nh_175
0.000000 -1.2020720588 -2.6132358634 -3.4354563750 1.5133618894 -3.9958935217 -1.6429270861 -5.5857139704 0.3632169199 -2.9238484403 -1.0627020402 -1.4499024497 1.9953641261 1.6217162456 -1.7173513397 3.7005849611 0.3164691241 1.8185656092 0.4517666341 -2.0799525295 -1.3742725297 -2.6199115118 -0.0006953246 -3.6684898087 -5.8372818252 4.0804445485 -0.7989971472 -2.9011766201 9.0621716934 3.7726145677 2.5796386160 0.6114868422 0.2031470927 -2.7963399025 3.0871463023 2.9250919400 3.1013838679 2.4944427624 2.0536587300 0.3524617497 -1.5154419166 0.9722353515 -1.9305647370 -5.3487027074 0.0375891273 -1.3158241381 0.9485138706 1.9664122891 2.8770343699 0.2612073347 -3.2046052898 -1.8065870687 19.0737856520 -1.0511160672 2.8076655707 -5.2589610209 1.2442394970 -0.4605847328 -3.1700264153 2.0694806317 -1.7057383347 4.0447219456 7.9696414609 -5.4416743063 2.4391526712 -2.0075972585 -1.1214467508 22.0438479666 -0.8245318294 0.8039123681 -1.9310717220 -3.0429780735 -3.7491144140 0.2947660318 -0.3334658349 3.7170495668 0.3572809012 1.4762859756 2.4388888600 0.0772143663 2.6037370607 1.9362237065 -3.6408171682 4.4846696506 0.0217135595 -3.0190670734 0.6221101524 3.1968590987 -0.3217256106 18.4251930423 2.0970549754 1.8839188003 1.1647970125 -4.0180899245 -0.7926914709 0.1036258948 -2.9355475969 1.9253272339 -3.6106175726 5.6106566630 -1.1331156467 1.1067463204 2.6675213057 -1.3685991990 1.6566272723 3.9113961644 3.3386173630 0.6841341840 2.2612907352 -1.6119683831 2.1607711967 -0.4644451686 -0.2558544328 -0.1124975686 -0.8455463923 -3.6579978383 -0.7404196819 -4.0619933475 -4.3351146508 -0.2464738142 -1.7086889476 3.5851534686 16.2251299411 4.4728144208 1.6072242056 -2.6389677020 3.8942890462 1.0567389672 0.7668775110 -1.8616166471 1.4839810344 1.4921450764 -3.4145631214 1.2466855501 -3.3961542767 0.9297819686 -1.8222841336 1.5545960707 3.7443114974 2.0859527582 -0.8211406326 1.1262225171 1.1604115566 5.3123775225 -0.8516539880 -4.9659694706 1.0411108481 1.7742538303 1.6475887839 1.6593430779 2.0207577851 0.4412743534 -3.1507918980 -0.8812577976 -0.0257426736 5.0833318781 1.8257401335 2.5538149225 -1.3203882808 1.6910486635 3.0650693544 1.3005644080 -1.9876355619 4.6078845851 -2.4093603520 -2.5877665707 -2.0560927119 2.6606717074 1.4670224832 0.3714495852 2.5620665631 2.3756521296 -1.6058567317 2.7687715639 -2.0322239057 0.5800390096 2.4144092630 1.8900713303 2.0252710505 -0.1012816703 -2.6923323823 -1.0733395872 -3.0853886170 1.2961382623 -0.5465260716 4.3805161523 -21.4064830732 1.6619333008 0.7020348104 -0.3248755112 -2.3053704530 3.1012525817 1.5640891761 -1.2699217062 -1.0649997914 -0.3908144251 -0.6985928620 1.2032530884 1.4732609105 -0.0510616792 -3.0205639709 -1.3089161472 1.4632164028 0.9504978635 5.7320135013 2.2548800892 -5.0417101249 3.8252593796 -0.8649002201 0.9321759707 -0.1227345610 0.4142313248 1.8614698715 -0.9030074801 7.9455847342 2.1159024168 0.8769273733 1.9438846307 -1.8213541671 -3.0314551586 0.5009760135 1.2365630545 -5.6861493001 -2.4169963582 -2.3492478764 -2.8394750787 -3.4219764848 2.0492236949 -3.9643534209 -2.8666742009 1.4198779207 1.2773067494 -1.5366951452 2.3623353346 0.1150840760 2.5059875294 -4.6182692548 3.6034380004 0.7113615959 -0.8239527330 -1.5428420667 -1.9930453809 -3.5635018082 -1.9053011857 0.5282380925 -1.3074030247 -0.2655378054 0.1461228729 0.7776154859 1.9114295348 -0.1015882064 1.2306951758 -2.3803100761 -4.5090048215 -0.3059600757 0.5355501977 -0.5396318039 1.8963599830 0.8846180299 -0.9618159348 0.7720887029 -2.3306518312 1.3445531494 -1.1128500849 0.9675660968 3.6511352700 0.2558843093 5.4819399332 -0.3808761036 1.2571372639 -0.7864537278 -0.9989566338 -4.3088174213 -3.3655401559 -0.0015732909 -1.7773614966 2.3070739989 -0.7512640214 0.2988493177 1.1683605425 0.3243383390 0.4264847472 0.8881206072 0.3044371449 -0.4168987881 -0.6346760772 0.7698302885 0.5988019340 0.9987904195 1.1106399516 0.6050748714 -0.0462047743 -1.3574359204 0.3494048480 1.0931675500 1.2536543132 0.4000858468 -0.8233857230 -0.7104263679 0.0959259130 1.5548795881 -0.4543010234 0.5696935285 3.3919477152 1.5043131597 1.9813114742 0.6801054793 -1.8680299071 -1.1556555140 0.7796808453 1.1592123649 1.1934100320 -0.1354535504 0.7152768352 0.2307171949 0.0405420724 2.0383051200 0.4598022706 -0.9326438134 -1.0374211958 -2.5708145244 1.2584993832 0.9014150135 -0.5366922650 -0.3721286728 -0.7996582865 -1.5576614140 0.2334397321 -1.1540008166 0.0690923505 -0.5708178988 -0.8076475273 0.0462896449 -2.3698892535 1.8681523465 0.6530935340 -1.9777355334 -0.9818058915 0.3597519867 -2.9773263712 -0.9612296428 0.6179118921 -0.7659369114 0.0699410283 -0.5206060705 0.8453667217 -1.3039427408 -0.1890361647 0.6962137806 -1.0606783356 0.4356775939 -0.3615509389 1.0698806178 -0.6383703240 -0.4476544859 0.7567029861 -1.7635785254 0.4175502977 1.4436250997 -1.1064932930 -1.0301961759 2.0115588309 -2.0948586013 -1.0048259972 -0.4875320185 -1.3688768483 -0.4556865866 -0.2026082329 -0.5267174602 -0.5670939959 0.2203534227 -1.3560767602 3.1667741710 -0.9062683931 1.7708392925 0.1488203385 0.1470732265 -0.8531854304 1.2566698168 0.5523221036 0.0215991171 -0.9375591212 0.7166218008 -1.8256394427 1.9993340678 -1.5786616413 -1.0852770882 -0.8617474037 1.2930835988 0.4211488489 -2.1299972707 0.1160585786 1.7103501815 -1.5021205586 0.4490906098 -0.9610273853 -0.5759100919 1.2659104725 -0.8664126114 -0.1387570000 1.3761890720 1.3995074710 -0.3847084880 -1.1793558381 0.4066724273 -0.6228103644 1.3715362988 -0.7271220272 -1.5404452173 -0.8717279337 -0.0886797976 -0.6768070908 0.1876754939 -0.5745373740 -0.7273195261 -0.9296269319 0.5555621458 0.2784818863 -0.5537813445 0.2748926564 1.4685874823 1.3350515989 0.1404808685 0.0227353796 -0.2959290302 0.6777103865 1.1909114496 0.0443490372 0.8941802771 -0.3969288269 -0.6350745517 0.1246277851 0.2555388758 -0.1383904746 13.4924065365 10.6496115172 0.3280451966 7.2066467242 -5.0800321287 -9.3682254161 -11.9103563254 -2.5156133963 4.3389885279 -7.9060452685 9.8483418378 -16.1218487709 5.8847364324 0.3685412659 -8.2586362912 -2.3127555428 10.5621596318 5.0921370573 -6.0839984557 -3.0008955829 -4.5371930301 4.9752769421 5.6208383045 -9.6179663244 -0.4250670521 -8.2487987040 7.6857258796 6.6609365705 7.8547146756 -6.7866477303 -3.9599407980 -2.5993058038 9.0505679000 0.2983807425 3.3249528920 5.8158841921 1.8866820967 -3.0755951253 -4.9292677987 -1.2224522643 -7.0693361922 2.9899155431 1.5392896655 -4.1773398163 -3.4699911823 4.4871269894 -7.1231266153 -4.1067381072 8.9586785862 5.8979493793 4.5132760429 -3.3539985281 3.4736370271 -1.2582599377 -9.0748516215 1.7124917748 2.0668590135 -7.3595342905 1.7961481193 -2.7882316712 -4.8697968601 5.9755927270 2.5368385718 -2.0135920291 5.9654502095 1.9012461021 0.8427776238 -8.9194152679 -13.0514044360 -1.6560879966 -3.8208349948 10.8937508254 -2.2628038879 2.7015390648 -6.3628229935 -1.9114455871 1.2068202980 -8.5560066070 12.0276095529 -20.1681446964 -9.6894199318 -6.5607381318 -7.8798557388 -5.5006844217 14.5899743685 2.7686013780 -8.2999955951 -2.0393103383 5.7660624968 9.4030167820 0.5644043950 0.0930153937 4.1585428721 -3.2959323781 -4.5658788463 -6.0460291347 -5.0505263448 0.6794305705 6.1110637528 1.8979683642 -5.7115158502 -3.1022020422 -2.3824228501 -1.9342284005 0.4122841236 -10.3875482318 9.4073746278 -3.8730417522 5.8492977020 -1.2793431760 -3.2483329225 -0.0594240304 -6.8176221397 6.1832766718 9.2611184015 -7.2483129246 8.0817839486 -13.0165364790 -2.5562446728 7.0627467496 1.6686387097 -6.0364577013 6.9354804837 -3.0912668037 12.0795112389 -1.0877659690 -4.5419207569 -0.1632202339 1.7553899493 5.1045265363 -4.4068652898 -2.5169692152 0.0516724211 -6.6186381808 -6.7002692716 -12.1968396986 2.5680913696 -5.3463345025 3.4119728103 1.0169859776 2.2146629692 -2.3928080618 11.5382296602 -1.8583111598 -2.2900759556 11.4910561878 -2.9961340175 -6.0249213101 -8.4665524582 5.1394139183 0.3845902762 0.8779114844 4.5959724403 14.6321203010 5.4529616279 4.0437386292
diff --git a/regtest/isdb/rt-cs2backbone/plumed.dat b/regtest/isdb/rt-cs2backbone/plumed.dat
index 8191a8b7bdfe4fb3b2a977fb29801c06f6afb68f..7ff047976b794394b1666637083baf14ad03e09f 100644
--- a/regtest/isdb/rt-cs2backbone/plumed.dat
+++ b/regtest/isdb/rt-cs2backbone/plumed.dat
@@ -1,4 +1,4 @@
-cs: CS2BACKBONE ATOMS=1-2612 NRES=176 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC
+cs: CS2BACKBONE ATOMS=1-2612 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC
ens: ENSEMBLE ARG=(cs\.ca_.*),(cs\.cb_.*),(cs\.hn_.*),(cs\.nh_.*)
@@ -9,11 +9,11 @@ RESTRAINT ARG=st.sqdevsum,ste.corr AT=0,1 KAPPA=0,0 SLOPE=1,1
DUMPFORCES ARG=(cs\.ca_.*),(cs\.cb_.*),(cs\.hn_.*),(cs\.nh_.*) FILE=forces
-csa: CS2BACKBONE ATOMS=1-2612 NRES=176 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC CAMSHIFT
+csa: CS2BACKBONE ATOMS=1-2612 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC CAMSHIFT
RESTRAINT ARG=csa AT=0 KAPPA=0 SLOPE=1.0
-PRINT ARG=csa,(cs\.ca_.*),(cs\.cb_.*),(cs\.hn_.*),(cs\.nh_.*) STRIDE=1 FILE=colvar FMT=%8.4f
+PRINT ARG=csa,(cs\.ca_.*),(cs\.cb_.*),(cs\.hn_.*),(cs\.nh_.*),(cs\.expca_.*),(cs\.expcb_.*),(cs\.exphn_.*),(cs\.expnh_.*) STRIDE=1 FILE=colvar FMT=%8.4f
PRINT ARG=ens.* STRIDE=1 FILE=ecolvar FMT=%8.4f
-#csn: CS2BACKBONE ATOMS=1-2612 NRES=176 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC CAMSHIFT NUMERICAL_DERIVATIVES
+#csn: CS2BACKBONE ATOMS=1-2612 DATADIR=../data/ TEMPLATE=template.pdb NEIGH_FREQ=1 NOPBC CAMSHIFT NUMERICAL_DERIVATIVES
#DUMPDERIVATIVES ARG=csa,csn FILE=derivatives1 FMT=%8.2f STRIDE=1
diff --git a/regtest/isdb/rt-noe-mi/COLVAR.reference b/regtest/isdb/rt-noe-mi/COLVAR.reference
index d5c5b125e983a0de7f93b0b140f7026e402ee812..4f64063eb695014b1da84aba78c711e809fb4033 100644
--- a/regtest/isdb/rt-noe-mi/COLVAR.reference
+++ b/regtest/isdb/rt-noe-mi/COLVAR.reference
@@ -1,13 +1,13 @@
#! FIELDS time prova.score mi.bias prova3.score mi2.bias
- 0.000000 679.722719 679.722719 0.000000 0.000000
- 0.050000 1943.550487 1943.550487 329.907600 329.907600
- 0.100000 1775.014770 1775.014770 270.630076 270.630076
- 0.150000 1809.604832 1809.604832 331.794820 331.794820
- 0.200000 4228.364674 4228.364674 8253.656692 8253.656692
- 0.250000 10.416057 10.416057 815.233597 815.233597
- 0.300000 392.257379 392.257379 1965.800728 1965.800728
- 0.350000 559.305807 559.305807 51.706769 51.706769
- 0.400000 671.998828 671.998828 2646.260645 2646.260645
- 0.450000 106.077295 106.077295 258.049622 258.049622
- 0.500000 1401.849524 1401.849524 129.510776 129.510776
- 0.550000 282.011310 282.011310 96.675304 96.675304
+ 0.000000 651.378799 651.378799 0.000000 0.000000
+ 0.050000 1910.954524 1910.954524 331.521832 331.521832
+ 0.100000 1760.207917 1760.207917 274.771218 274.771218
+ 0.150000 1960.598572 1960.598572 459.047460 459.047460
+ 0.200000 4469.406463 4469.406463 8457.173610 8457.173610
+ 0.250000 236.609258 236.609258 1005.998859 1005.998859
+ 0.300000 1551.144706 1551.144706 3004.243046 3004.243046
+ 0.350000 730.509542 730.509542 195.825158 195.825158
+ 0.400000 699.429399 699.429399 2676.602124 2676.602124
+ 0.450000 198.505698 198.505698 337.632250 337.632250
+ 0.500000 1368.741397 1368.741397 138.877834 138.877834
+ 0.550000 350.403008 350.403008 157.423796 157.423796
diff --git a/regtest/isdb/rt-noe-mi/deriv.reference b/regtest/isdb/rt-noe-mi/deriv.reference
index 49da39a23cedb35367f595b1d4aeb9ac3c8668b4..e52b04f0781d543b0118495ad75a23769cf93e66 100644
--- a/regtest/isdb/rt-noe-mi/deriv.reference
+++ b/regtest/isdb/rt-noe-mi/deriv.reference
@@ -1,325 +1,325 @@
#! FIELDS time parameter prova.score prova3.score
- 0.000000 0 -97.303 0.000
- 0.000000 1 111.578 0.000
- 0.000000 2 -15.333 0.000
- 0.000000 3 -176.802 0.000
- 0.000000 4 154.764 0.000
- 0.000000 5 17.816 0.000
+ 0.000000 0 -24.818 0.000
+ 0.000000 1 28.460 0.000
+ 0.000000 2 -3.911 0.000
+ 0.000000 3 -45.096 0.000
+ 0.000000 4 39.475 0.000
+ 0.000000 5 4.544 0.000
0.000000 6 -12358.981 0.000
0.000000 7 9194.912 0.000
0.000000 8 -278.714 0.000
- 0.000000 9 97.303 0.000
- 0.000000 10 -111.578 0.000
- 0.000000 11 15.333 0.000
- 0.000000 12 176.802 0.000
- 0.000000 13 -154.764 0.000
- 0.000000 14 -17.816 0.000
+ 0.000000 9 24.818 0.000
+ 0.000000 10 -28.460 0.000
+ 0.000000 11 3.911 0.000
+ 0.000000 12 45.096 0.000
+ 0.000000 13 -39.475 0.000
+ 0.000000 14 -4.544 0.000
0.000000 15 12358.981 0.000
0.000000 16 -9194.912 0.000
0.000000 17 278.714 0.000
- 0.000000 18 -5907.686 0.000
- 0.000000 19 4429.473 0.000
- 0.000000 20 -127.733 0.000
- 0.000000 21 4429.473 0.000
- 0.000000 22 -3331.110 0.000
- 0.000000 23 96.985 0.000
- 0.000000 24 -127.733 0.000
- 0.000000 25 96.985 0.000
- 0.000000 26 -5.246 0.000
- 0.050000 0 123.408 14.837
- 0.050000 1 -88.637 -10.657
- 0.050000 2 -120.597 -14.499
- 0.050000 3 88.767 10.672
- 0.050000 4 -103.718 -12.470
- 0.050000 5 -89.324 -10.739
+ 0.000000 18 -5793.454 0.000
+ 0.000000 19 4318.982 0.000
+ 0.000000 20 -129.250 0.000
+ 0.000000 21 4318.982 0.000
+ 0.000000 22 -3222.355 0.000
+ 0.000000 23 96.658 0.000
+ 0.000000 24 -129.250 0.000
+ 0.000000 25 96.658 0.000
+ 0.000000 26 -3.518 0.000
+ 0.050000 0 87.040 59.348
+ 0.050000 1 -62.516 -42.626
+ 0.050000 2 -85.058 -57.996
+ 0.050000 3 62.608 42.689
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+ 0.050000 5 -63.001 -42.957
0.050000 6 5826.440 2421.846
0.050000 7 -5272.667 -2191.662
0.050000 8 -3219.351 -1338.171
- 0.050000 9 -123.408 -14.837
- 0.050000 10 88.637 10.657
- 0.050000 11 120.597 14.499
- 0.050000 12 -88.767 -10.672
- 0.050000 13 103.718 12.470
- 0.050000 14 89.324 10.739
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+ 0.050000 10 62.516 42.626
+ 0.050000 11 85.058 57.996
+ 0.050000 12 -62.608 -42.689
+ 0.050000 13 73.153 49.879
+ 0.050000 14 63.001 42.957
0.050000 15 -5826.440 -2421.846
0.050000 16 5272.667 2191.662
0.050000 17 3219.351 1338.171
- 0.050000 18 -2830.425 -1146.230
- 0.050000 19 2560.115 1037.131
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- 0.050000 21 2560.115 1037.131
- 0.050000 22 -2320.562 -939.011
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- 0.050000 24 1608.603 638.711
- 0.050000 25 -1454.754 -577.889
- 0.050000 26 -933.000 -358.226
- 0.100000 0 -209.249 58.635
- 0.100000 1 52.954 -14.839
- 0.100000 2 -103.471 28.994
- 0.100000 3 -143.942 40.335
- 0.100000 4 19.450 -5.450
- 0.100000 5 -39.819 11.158
+ 0.050000 18 -2800.223 -1183.195
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+ 0.050000 20 1578.750 675.249
+ 0.050000 21 2533.165 1070.116
+ 0.050000 22 -2295.061 -970.221
+ 0.050000 23 -1428.021 -610.608
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+ 0.050000 25 -1428.021 -610.608
+ 0.050000 26 -903.486 -394.350
+ 0.100000 0 166.212 234.539
+ 0.100000 1 -42.063 -59.354
+ 0.100000 2 82.189 115.976
+ 0.100000 3 114.337 161.339
+ 0.100000 4 -15.450 -21.801
+ 0.100000 5 31.629 44.632
0.100000 6 -8902.412 -3484.542
0.100000 7 3373.973 1320.625
0.100000 8 -1686.987 -660.313
- 0.100000 9 209.249 -58.635
- 0.100000 10 -52.954 14.839
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- 0.100000 12 143.942 -40.335
- 0.100000 13 -19.450 5.450
- 0.100000 14 39.819 -11.158
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+ 0.100000 13 15.450 21.801
+ 0.100000 14 -31.629 -44.632
0.100000 15 8902.412 3484.542
0.100000 16 -3373.973 -1320.625
0.100000 17 1686.987 660.313
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+ 0.450000 18 -480.026 2662.595
+ 0.450000 19 272.493 -1221.982
+ 0.450000 20 1222.465 -4353.062
+ 0.450000 21 272.493 -1221.982
+ 0.450000 22 -123.516 589.114
+ 0.450000 23 -607.748 2047.428
+ 0.450000 24 1222.465 -4353.062
+ 0.450000 25 -607.748 2047.428
+ 0.450000 26 -2616.224 7290.884
+ 0.500000 0 124.953 104.677
+ 0.500000 1 -9.303 -7.793
+ 0.500000 2 -44.607 -37.368
+ 0.500000 3 210.164 176.061
+ 0.500000 4 15.990 13.396
+ 0.500000 5 -41.705 -34.938
0.500000 6 12370.768 3783.829
0.500000 7 1326.297 405.672
0.500000 8 -1930.432 -590.458
- 0.500000 9 -105.664 -26.169
- 0.500000 10 7.867 1.948
- 0.500000 11 37.721 9.342
- 0.500000 12 -177.722 -44.015
- 0.500000 13 -13.522 -3.349
- 0.500000 14 35.267 8.734
+ 0.500000 9 -124.953 -104.677
+ 0.500000 10 9.303 7.793
+ 0.500000 11 44.607 37.368
+ 0.500000 12 -210.164 -176.061
+ 0.500000 13 -15.990 -13.396
+ 0.500000 14 41.705 34.938
0.500000 15 -12370.768 -3783.829
0.500000 16 -1326.297 -405.672
0.500000 17 1930.432 590.458
- 0.500000 18 -7881.585 -2397.254
- 0.500000 19 -824.571 -251.955
- 0.500000 20 1253.647 379.967
- 0.500000 21 -824.571 -251.955
- 0.500000 22 -89.252 -27.223
- 0.500000 23 127.822 39.106
- 0.500000 24 1253.647 379.967
- 0.500000 25 127.822 39.106
- 0.500000 26 -203.139 -61.153
- 0.550000 0 27.057 -140.307
- 0.550000 1 -23.924 124.057
- 0.550000 2 -4.700 24.375
- 0.550000 3 83.682 -433.937
- 0.550000 4 -57.708 299.245
- 0.550000 5 4.564 -23.666
+ 0.500000 18 -7923.845 -2569.258
+ 0.500000 19 -825.372 -255.216
+ 0.500000 20 1264.576 424.448
+ 0.500000 21 -825.372 -255.216
+ 0.500000 22 -89.493 -28.202
+ 0.500000 23 127.791 38.983
+ 0.500000 24 1264.576 424.448
+ 0.500000 25 127.791 38.983
+ 0.500000 26 -206.215 -73.674
+ 0.550000 0 -518.539 -561.227
+ 0.550000 1 458.484 496.229
+ 0.550000 2 90.082 97.498
+ 0.550000 3 -1603.723 -1735.748
+ 0.550000 4 1105.935 1196.980
+ 0.550000 5 -87.465 -94.666
0.550000 6 12453.405 -6491.656
0.550000 7 -4814.129 2509.488
0.550000 8 3267.967 -1703.512
- 0.550000 9 -27.057 140.307
- 0.550000 10 23.924 -124.057
- 0.550000 11 4.700 -24.375
- 0.550000 12 -83.682 433.937
- 0.550000 13 57.708 -299.245
- 0.550000 14 -4.564 23.666
+ 0.550000 9 518.539 561.227
+ 0.550000 10 -458.484 -496.229
+ 0.550000 11 -90.082 -97.498
+ 0.550000 12 1603.723 1735.748
+ 0.550000 13 -1105.935 -1196.980
+ 0.550000 14 87.465 94.666
0.550000 15 -12453.405 6491.656
0.550000 16 4814.129 -2509.488
0.550000 17 -3267.967 1703.512
- 0.550000 18 -6330.234 3585.202
- 0.550000 19 2468.639 -1497.695
- 0.550000 20 -1644.902 856.547
- 0.550000 21 2468.639 -1497.695
- 0.550000 22 -970.665 663.800
- 0.550000 23 635.291 -328.102
- 0.550000 24 -1644.902 856.547
- 0.550000 25 635.291 -328.102
- 0.550000 26 -432.301 228.160
+ 0.550000 18 -5096.373 4537.110
+ 0.550000 19 1557.080 -2200.951
+ 0.550000 20 -1648.795 853.543
+ 0.550000 21 1557.080 -2200.951
+ 0.550000 22 -288.395 1190.162
+ 0.550000 23 648.517 -317.898
+ 0.550000 24 -1648.795 853.543
+ 0.550000 25 648.517 -317.898
+ 0.550000 26 -420.147 237.536
diff --git a/regtest/isdb/rt-noe-mpi/COLVAR.0.reference b/regtest/isdb/rt-noe-mpi/COLVAR.0.reference
index 685c3bcbcae6392de4f57d59aec23c76d84f75e5..e4fb06c3dc7ead72ebbe6fb5652d704bb478d17e 100644
--- a/regtest/isdb/rt-noe-mpi/COLVAR.0.reference
+++ b/regtest/isdb/rt-noe-mpi/COLVAR.0.reference
@@ -1,13 +1,13 @@
#! FIELDS time inver1 inver2 test prova.exp_0 prova.exp_1 st1.sqdevsum st2.sqdevsum
- 0.000000 0.108991 0.133453 0.133462 0.500000 0.400000 0.223935 0.223935
- 0.050000 0.109013 0.133441 0.133431 0.500000 0.400000 0.223924 0.223924
- 0.100000 0.108989 0.133449 0.133478 0.500000 0.400000 0.223939 0.223939
- 0.150000 0.108955 0.133496 0.133526 0.500000 0.400000 0.223941 0.223941
- 0.200000 0.109006 0.133528 0.133541 0.500000 0.400000 0.223884 0.223884
- 0.250000 0.109049 0.133507 0.133485 0.500000 0.400000 0.223861 0.223861
- 0.300000 0.109026 0.133512 0.133550 0.500000 0.400000 0.223876 0.223876
- 0.350000 0.109015 0.133560 0.133582 0.500000 0.400000 0.223859 0.223859
- 0.400000 0.108984 0.133554 0.133537 0.500000 0.400000 0.223887 0.223887
- 0.450000 0.108969 0.133494 0.133462 0.500000 0.400000 0.223931 0.223931
- 0.500000 0.108994 0.133489 0.133526 0.500000 0.400000 0.223914 0.223914
- 0.550000 0.108989 0.133486 0.133455 0.500000 0.400000 0.223920 0.223920
+ 0.000000 0.097100 0.133453 0.133462 0.500000 0.400000 0.233376 0.233376
+ 0.050000 0.097120 0.133441 0.133431 0.500000 0.400000 0.233366 0.233366
+ 0.100000 0.097098 0.133449 0.133478 0.500000 0.400000 0.233379 0.233379
+ 0.150000 0.097067 0.133496 0.133526 0.500000 0.400000 0.233379 0.233379
+ 0.200000 0.097113 0.133528 0.133541 0.500000 0.400000 0.233325 0.233325
+ 0.250000 0.097152 0.133507 0.133485 0.500000 0.400000 0.233305 0.233305
+ 0.300000 0.097131 0.133512 0.133550 0.500000 0.400000 0.233319 0.233319
+ 0.350000 0.097121 0.133560 0.133582 0.500000 0.400000 0.233301 0.233301
+ 0.400000 0.097093 0.133554 0.133537 0.500000 0.400000 0.233327 0.233327
+ 0.450000 0.097080 0.133494 0.133462 0.500000 0.400000 0.233370 0.233370
+ 0.500000 0.097102 0.133489 0.133526 0.500000 0.400000 0.233355 0.233355
+ 0.550000 0.097098 0.133486 0.133455 0.500000 0.400000 0.233360 0.233360
diff --git a/regtest/isdb/rt-noe-mpi/COLVAR.1.reference b/regtest/isdb/rt-noe-mpi/COLVAR.1.reference
index a9abb0736e4a5e06d70a1a987b55426e55121b15..78e4350c79cb7c1791c55e3c99ef0dc8ccdab591 100644
--- a/regtest/isdb/rt-noe-mpi/COLVAR.1.reference
+++ b/regtest/isdb/rt-noe-mpi/COLVAR.1.reference
@@ -1,13 +1,13 @@
#! FIELDS time inver1 inver2 test prova.exp_0 prova.exp_1 st1.sqdevsum st2.sqdevsum
- 0.000000 0.108991 0.133453 0.133455 0.500000 0.400000 0.223935 0.223935
- 0.050000 0.109013 0.133441 0.133462 0.500000 0.400000 0.223924 0.223924
- 0.100000 0.108989 0.133449 0.133431 0.500000 0.400000 0.223939 0.223939
- 0.150000 0.108955 0.133496 0.133478 0.500000 0.400000 0.223941 0.223941
- 0.200000 0.109006 0.133528 0.133526 0.500000 0.400000 0.223884 0.223884
- 0.250000 0.109049 0.133507 0.133541 0.500000 0.400000 0.223861 0.223861
- 0.300000 0.109026 0.133512 0.133485 0.500000 0.400000 0.223876 0.223876
- 0.350000 0.109015 0.133560 0.133550 0.500000 0.400000 0.223859 0.223859
- 0.400000 0.108984 0.133554 0.133582 0.500000 0.400000 0.223887 0.223887
- 0.450000 0.108969 0.133494 0.133537 0.500000 0.400000 0.223931 0.223931
- 0.500000 0.108994 0.133489 0.133462 0.500000 0.400000 0.223914 0.223914
- 0.550000 0.108989 0.133486 0.133526 0.500000 0.400000 0.223920 0.223920
+ 0.000000 0.097100 0.133453 0.133455 0.500000 0.400000 0.233376 0.233376
+ 0.050000 0.097120 0.133441 0.133462 0.500000 0.400000 0.233366 0.233366
+ 0.100000 0.097098 0.133449 0.133431 0.500000 0.400000 0.233379 0.233379
+ 0.150000 0.097067 0.133496 0.133478 0.500000 0.400000 0.233379 0.233379
+ 0.200000 0.097113 0.133528 0.133526 0.500000 0.400000 0.233325 0.233325
+ 0.250000 0.097152 0.133507 0.133541 0.500000 0.400000 0.233305 0.233305
+ 0.300000 0.097131 0.133512 0.133485 0.500000 0.400000 0.233319 0.233319
+ 0.350000 0.097121 0.133560 0.133550 0.500000 0.400000 0.233301 0.233301
+ 0.400000 0.097093 0.133554 0.133582 0.500000 0.400000 0.233327 0.233327
+ 0.450000 0.097080 0.133494 0.133537 0.500000 0.400000 0.233370 0.233370
+ 0.500000 0.097102 0.133489 0.133462 0.500000 0.400000 0.233355 0.233355
+ 0.550000 0.097098 0.133486 0.133526 0.500000 0.400000 0.233360 0.233360
diff --git a/regtest/isdb/rt-noe-mpi/forces.0.reference b/regtest/isdb/rt-noe-mpi/forces.0.reference
index aa549611195a85c79e5ac1545bc3e772e25cd7b3..1e13e396aa59380606371a65874c21c3dc20524d 100644
--- a/regtest/isdb/rt-noe-mpi/forces.0.reference
+++ b/regtest/isdb/rt-noe-mpi/forces.0.reference
@@ -1,13 +1,13 @@
#! FIELDS time prova.noe_0 prova.noe_1 prova2.noe_0 prova2.noe_1
- 0.000000 -0.0000000119 -0.0000000335 -0.0000000119 -0.0000000335
- 0.050000 -0.0000000119 -0.0000000335 -0.0000000119 -0.0000000335
- 0.100000 -0.0000000119 -0.0000000335 -0.0000000119 -0.0000000335
- 0.150000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.200000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.250000 -0.0000000120 -0.0000000336 -0.0000000120 -0.0000000336
- 0.300000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.350000 -0.0000000119 -0.0000000337 -0.0000000119 -0.0000000337
- 0.400000 -0.0000000119 -0.0000000337 -0.0000000119 -0.0000000337
- 0.450000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.500000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.550000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
+ 0.000000 -0.0000000055 -0.0000000335 -0.0000000055 -0.0000000335
+ 0.050000 -0.0000000055 -0.0000000335 -0.0000000055 -0.0000000335
+ 0.100000 -0.0000000055 -0.0000000335 -0.0000000055 -0.0000000335
+ 0.150000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.200000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.250000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.300000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.350000 -0.0000000055 -0.0000000337 -0.0000000055 -0.0000000337
+ 0.400000 -0.0000000055 -0.0000000337 -0.0000000055 -0.0000000337
+ 0.450000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.500000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.550000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
diff --git a/regtest/isdb/rt-noe-mpi/forces.1.reference b/regtest/isdb/rt-noe-mpi/forces.1.reference
index aa549611195a85c79e5ac1545bc3e772e25cd7b3..1e13e396aa59380606371a65874c21c3dc20524d 100644
--- a/regtest/isdb/rt-noe-mpi/forces.1.reference
+++ b/regtest/isdb/rt-noe-mpi/forces.1.reference
@@ -1,13 +1,13 @@
#! FIELDS time prova.noe_0 prova.noe_1 prova2.noe_0 prova2.noe_1
- 0.000000 -0.0000000119 -0.0000000335 -0.0000000119 -0.0000000335
- 0.050000 -0.0000000119 -0.0000000335 -0.0000000119 -0.0000000335
- 0.100000 -0.0000000119 -0.0000000335 -0.0000000119 -0.0000000335
- 0.150000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.200000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.250000 -0.0000000120 -0.0000000336 -0.0000000120 -0.0000000336
- 0.300000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.350000 -0.0000000119 -0.0000000337 -0.0000000119 -0.0000000337
- 0.400000 -0.0000000119 -0.0000000337 -0.0000000119 -0.0000000337
- 0.450000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.500000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
- 0.550000 -0.0000000119 -0.0000000336 -0.0000000119 -0.0000000336
+ 0.000000 -0.0000000055 -0.0000000335 -0.0000000055 -0.0000000335
+ 0.050000 -0.0000000055 -0.0000000335 -0.0000000055 -0.0000000335
+ 0.100000 -0.0000000055 -0.0000000335 -0.0000000055 -0.0000000335
+ 0.150000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.200000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.250000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.300000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.350000 -0.0000000055 -0.0000000337 -0.0000000055 -0.0000000337
+ 0.400000 -0.0000000055 -0.0000000337 -0.0000000055 -0.0000000337
+ 0.450000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.500000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
+ 0.550000 -0.0000000055 -0.0000000336 -0.0000000055 -0.0000000336
diff --git a/regtest/isdb/rt-noe/COLVAR.reference b/regtest/isdb/rt-noe/COLVAR.reference
index 778c518f95c640f32ac8b15b158658234e31ebc5..b4be81d3c93a9d68196324318b8152b90eb57ed0 100644
--- a/regtest/isdb/rt-noe/COLVAR.reference
+++ b/regtest/isdb/rt-noe/COLVAR.reference
@@ -1,13 +1,13 @@
#! FIELDS time prova.noe_0 prova.noe_1 prova.exp_0 prova.exp_1
- 0.000000 4.193510 26.154650 0.500000 0.400000
- 0.050000 3.536670 9.903690 0.500000 0.400000
- 0.100000 5.245561 11.461500 0.500000 0.400000
- 0.150000 10.025410 10.922209 0.500000 0.400000
- 0.200000 11.568763 107.170189 0.500000 0.400000
- 0.250000 11.333972 50.704210 0.500000 0.400000
- 0.300000 20.853236 62.191624 0.500000 0.400000
- 0.350000 10.399861 27.869439 0.500000 0.400000
- 0.400000 7.041215 72.129687 0.500000 0.400000
- 0.450000 8.805473 39.779555 0.500000 0.400000
- 0.500000 2.611249 16.087861 0.500000 0.400000
- 0.550000 8.222947 33.982767 0.500000 0.400000
+ 0.000000 8.387020 26.154650 0.500000 0.400000
+ 0.050000 7.073340 9.903690 0.500000 0.400000
+ 0.100000 10.491122 11.461500 0.500000 0.400000
+ 0.150000 20.050820 10.922209 0.500000 0.400000
+ 0.200000 23.137526 107.170189 0.500000 0.400000
+ 0.250000 22.667944 50.704210 0.500000 0.400000
+ 0.300000 41.706472 62.191624 0.500000 0.400000
+ 0.350000 20.799723 27.869439 0.500000 0.400000
+ 0.400000 14.082431 72.129687 0.500000 0.400000
+ 0.450000 17.610946 39.779555 0.500000 0.400000
+ 0.500000 5.222497 16.087861 0.500000 0.400000
+ 0.550000 16.445895 33.982767 0.500000 0.400000
diff --git a/regtest/isdb/rt-noe/deriv.reference b/regtest/isdb/rt-noe/deriv.reference
index 982e1ba164dce153f13776100349ba0e47225a7a..3686c8c19ca8cd81dce508cf0d5c61d45904e7c9 100644
--- a/regtest/isdb/rt-noe/deriv.reference
+++ b/regtest/isdb/rt-noe/deriv.reference
@@ -1,325 +1,325 @@
#! FIELDS time parameter prova.noe_0 provan.noe_0 prova.noe_1 provan.noe_1
- 0.000000 0 8 8 0 0
- 0.000000 1 -9 -9 0 0
- 0.000000 2 1 1 0 0
- 0.000000 3 15 15 0 0
- 0.000000 4 -13 -13 0 0
- 0.000000 5 -1 -1 0 0
+ 0.000000 0 16 16 0 0
+ 0.000000 1 -19 -19 0 0
+ 0.000000 2 3 3 0 0
+ 0.000000 3 29 29 0 0
+ 0.000000 4 -26 -26 0 0
+ 0.000000 5 -3 -3 0 0
0.000000 6 0 0 217 217
0.000000 7 0 0 -161 -161
0.000000 8 0 0 5 5
- 0.000000 9 -8 -8 0 0
- 0.000000 10 9 9 0 0
- 0.000000 11 -1 -1 0 0
- 0.000000 12 -15 -15 0 0
- 0.000000 13 13 13 0 0
- 0.000000 14 1 1 0 0
+ 0.000000 9 -16 -16 0 0
+ 0.000000 10 19 19 0 0
+ 0.000000 11 -3 -3 0 0
+ 0.000000 12 -29 -29 0 0
+ 0.000000 13 26 26 0 0
+ 0.000000 14 3 3 0 0
0.000000 15 0 0 -217 -217
0.000000 16 0 0 161 161
0.000000 17 0 0 -5 -5
- 0.000000 18 13 13 101 101
- 0.000000 19 -12 -12 -75 -75
+ 0.000000 18 26 26 101 101
+ 0.000000 19 -25 -25 -75 -75
0.000000 20 -0 -0 2 2
- 0.000000 21 -12 -12 -75 -75
- 0.000000 22 12 12 56 56
+ 0.000000 21 -25 -25 -75 -75
+ 0.000000 22 24 24 56 56
0.000000 23 -0 -0 -2 -2
0.000000 24 -0 -0 2 2
0.000000 25 -0 -0 -2 -2
0.000000 26 0 0 0 0
- 0.050000 0 -9 -9 0 0
- 0.050000 1 7 7 0 0
- 0.050000 2 9 9 0 0
- 0.050000 3 -7 -7 0 0
- 0.050000 4 8 8 0 0
- 0.050000 5 7 7 0 0
+ 0.050000 0 -18 -18 0 0
+ 0.050000 1 13 13 0 0
+ 0.050000 2 18 18 0 0
+ 0.050000 3 -13 -13 0 0
+ 0.050000 4 15 15 0 0
+ 0.050000 5 13 13 0 0
0.050000 6 0 0 -60 -60
0.050000 7 0 0 54 54
0.050000 8 0 0 33 33
- 0.050000 9 9 9 0 0
- 0.050000 10 -7 -7 0 0
- 0.050000 11 -9 -9 0 0
- 0.050000 12 7 7 0 0
- 0.050000 13 -8 -8 0 0
- 0.050000 14 -7 -7 0 0
+ 0.050000 9 18 18 0 0
+ 0.050000 10 -13 -13 0 0
+ 0.050000 11 -18 -18 0 0
+ 0.050000 12 13 13 0 0
+ 0.050000 13 -15 -15 0 0
+ 0.050000 14 -13 -13 0 0
0.050000 15 0 0 60 60
0.050000 16 0 0 -54 -54
0.050000 17 0 0 -33 -33
- 0.050000 18 8 8 28 28
- 0.050000 19 -7 -7 -25 -25
- 0.050000 20 -7 -7 -15 -15
- 0.050000 21 -7 -7 -25 -25
- 0.050000 22 6 6 23 23
- 0.050000 23 7 7 14 14
- 0.050000 24 -7 -7 -15 -15
- 0.050000 25 7 7 14 14
- 0.050000 26 7 7 9 9
- 0.100000 0 22 22 0 0
- 0.100000 1 -6 -6 0 0
- 0.100000 2 11 11 0 0
- 0.100000 3 15 15 0 0
- 0.100000 4 -2 -2 0 0
- 0.100000 5 4 4 0 0
+ 0.050000 18 15 15 28 28
+ 0.050000 19 -13 -13 -25 -25
+ 0.050000 20 -15 -15 -15 -15
+ 0.050000 21 -13 -13 -25 -25
+ 0.050000 22 13 13 23 23
+ 0.050000 23 13 13 14 14
+ 0.050000 24 -15 -15 -15 -15
+ 0.050000 25 13 13 14 14
+ 0.050000 26 15 15 9 9
+ 0.100000 0 45 45 0 0
+ 0.100000 1 -11 -11 0 0
+ 0.100000 2 22 22 0 0
+ 0.100000 3 31 31 0 0
+ 0.100000 4 -4 -4 0 0
+ 0.100000 5 9 9 0 0
0.100000 6 0 0 95 95
0.100000 7 0 0 -36 -36
0.100000 8 0 0 18 18
- 0.100000 9 -22 -22 0 0
- 0.100000 10 6 6 0 0
- 0.100000 11 -11 -11 0 0
- 0.100000 12 -15 -15 0 0
- 0.100000 13 2 2 0 0
- 0.100000 14 -4 -4 0 0
+ 0.100000 9 -45 -45 0 0
+ 0.100000 10 11 11 0 0
+ 0.100000 11 -22 -22 0 0
+ 0.100000 12 -31 -31 0 0
+ 0.100000 13 4 4 0 0
+ 0.100000 14 -9 -9 0 0
0.100000 15 0 0 -95 -95
0.100000 16 0 0 36 36
0.100000 17 0 0 -18 -18
- 0.100000 18 26 26 58 58
- 0.100000 19 -5 -5 -22 -22
- 0.100000 20 10 10 11 11
- 0.100000 21 -5 -5 -22 -22
- 0.100000 22 1 1 8 8
- 0.100000 23 -2 -2 -4 -4
- 0.100000 24 10 10 11 11
- 0.100000 25 -2 -2 -4 -4
- 0.100000 26 4 4 2 2
- 0.150000 0 -31 -31 0 0
- 0.150000 1 59 59 0 0
- 0.150000 2 -29 -29 0 0
- 0.150000 3 -9 -9 0 0
- 0.150000 4 15 15 0 0
- 0.150000 5 -4 -4 0 0
+ 0.100000 18 52 52 58 58
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0.550000 15 0 0 332 332
0.550000 16 0 0 -129 -129
0.550000 17 0 0 87 87
- 0.550000 18 32 32 167 167
- 0.550000 19 -23 -23 -65 -65
+ 0.550000 18 63 63 167 167
+ 0.550000 19 -47 -47 -65 -65
0.550000 20 -0 -0 44 44
- 0.550000 21 -23 -23 -65 -65
- 0.550000 22 17 17 25 25
- 0.550000 23 0 0 -17 -17
+ 0.550000 21 -47 -47 -65 -65
+ 0.550000 22 35 35 25 25
+ 0.550000 23 1 1 -17 -17
0.550000 24 -0 -0 44 44
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diff --git a/regtest/scripts/check b/regtest/scripts/check
index 7d35f64e86ef5be76bf5097b25cdae4288ba8c17..3d9360bf70e1fbfea626d265e84d4a418038ec3f 100755
--- a/regtest/scripts/check
+++ b/regtest/scripts/check
@@ -30,8 +30,8 @@ dirs=$(
done
)
-file1=$(mktemp)
-file2=$(mktemp)
+file1=$(mktemp -t plumed.XXXXXX)
+file2=$(mktemp -t plumed.XXXXXX)
for dir in $dirs
do
diff --git a/regtest/scripts/what b/regtest/scripts/what
index ed38be884057dc04db8518199cf8bf236aa6b25c..bfff7fabd010e10cb0ade2c64e1f31d05fd20c5a 100755
--- a/regtest/scripts/what
+++ b/regtest/scripts/what
@@ -1,7 +1,13 @@
#!/bin/bash
+if test -n "$PLUMED_PREPEND_PATH" ; then
+ PATH="$PLUMED_PREPEND_PATH:$PATH"
+fi
+
+plumed="${PLUMED_PROGRAM_NAME:-plumed}"
+
for action in $(
- cat $(plumed info --root)/src/*/*.cpp | grep PLUMED_REGISTER_ACTION |
+ cat $($plumed --no-mpi info --root)/src/*/*.cpp | grep PLUMED_REGISTER_ACTION |
sed -e 's/,/ /g
s/(/ /g
s/)/ /g' | awk '{print $3}' | sed -e 's/\([\"]\)//g'
diff --git a/regtest/trajectories/HILLS_t2 b/regtest/trajectories/HILLS_t2
index 13d4e9e9faa4b6bdec746821bcc6deea396b9070..fc25daac4676cc5341fe6589a033df6eed0bf887 100644
--- a/regtest/trajectories/HILLS_t2
+++ b/regtest/trajectories/HILLS_t2
@@ -1,6 +1,5 @@
#! FIELDS time t1 t2 sigma_t1_t1 sigma_t2_t2 sigma_t2_t1 height biasf
#! SET multivariate true
-#! SET kerneltype gaussian
#! SET min_t1 -pi
#! SET max_t1 pi
#! SET min_t2 -pi
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/Makefile b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/bias.ves1.iter-10.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/bias.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..b0a9211f50b09e6483820b2fe85a30aa141c1b53
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/bias.ves1.iter-10.data.reference
@@ -0,0 +1,106 @@
+#! FIELDS phi2 ves1.bias der_phi2
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+ -3.141592654 -8.556547577 -143.876631181
+ -3.078760801 -1.624820878 -80.248724746
+ -3.015928947 1.920155818 -35.376009797
+ -2.953097094 3.132042319 -5.390156079
+ -2.890265241 2.840137030 12.993512501
+ -2.827433388 1.683966005 22.541402115
+ -2.764601535 0.143933965 25.561668570
+ -2.701769682 -1.431635370 23.959179684
+ -2.638937829 -2.802761251 19.285716871
+ -2.576105976 -3.817080061 12.785701486
+ -2.513274123 -4.391859180 5.437720791
+ -2.450442270 -4.498495000 -2.007882101
+ -2.387610417 -4.149255796 -8.995100239
+ -2.324778564 -3.386045849 -15.131792864
+ -2.261946711 -2.270982197 -20.162419446
+ -2.199114858 -0.878589792 -23.943753459
+ -2.136283004 0.710565358 -26.423361168
+ -2.073451151 2.414972291 -27.620640092
+ -2.010619298 4.156155063 -27.610220941
+ -1.947787445 5.861679161 -26.507545869
+ -1.884955592 7.467315443 -24.456444621
+ -1.822123739 8.918481773 -21.618538827
+ -1.759291886 10.171072081 -18.164313061
+ -1.696460033 11.191772750 -14.265699571
+ -1.633628180 11.957956808 -10.090031579
+ -1.570796327 12.457237589 -5.795227962
+ -1.507964474 12.686755103 -1.526079751
+ -1.445132621 12.652260485 2.588483609
+ -1.382300768 12.367056434 6.437263014
+ -1.319468915 11.850844569 9.927901118
+ -1.256637061 11.128524095 12.987337197
+ -1.193805208 10.228980029 15.561699435
+ -1.130973355 9.183893570 17.615722152
+ -1.068141502 8.026601860 19.131769077
+ -1.005309649 6.791029521 20.108537643
+ -0.942477796 5.510709801 20.559513284
+ -0.879645943 4.217909015 20.511236954
+ -0.816814090 2.942864204 20.001443443
+ -0.753982237 1.713140428 19.077122717
+ -0.691150384 0.553111052 17.792551227
+ -0.628318531 -0.516438433 16.207335135
+ -0.565486678 -1.478585015 14.384502554
+ -0.502654825 -2.320425279 12.388677225
+ -0.439822972 -3.033121097 10.284361608
+ -0.376991118 -3.611841487 8.134353061
+ -0.314159265 -4.055609685 5.998312718
+ -0.251327412 -4.367065494 3.931502730
+ -0.188495559 -4.552153919 1.983703866
+ -0.125663706 -4.619751681 0.198321904
+ -0.062831853 -4.581243659 -1.388312076
+ 0.000000000 -4.450061522 -2.747445534
+ 0.062831853 -4.241196831 -3.858213473
+ 0.125663706 -3.970700760 -4.707756362
+ 0.188495559 -3.655182251 -5.291153362
+ 0.251327412 -3.311315943 -5.611179607
+ 0.314159265 -2.955370591 -5.677898533
+ 0.376991118 -2.602767955 -5.508102226
+ 0.439822972 -2.267681240 -5.124614638
+ 0.502654825 -1.962681198 -4.555474129
+ 0.565486678 -1.698436914 -3.833013275
+ 0.628318531 -1.483477146 -2.992855131
+ 0.691150384 -1.324016817 -2.072846225
+ 0.753982237 -1.223851992 -1.111947464
+ 0.816814090 -1.184325291 -0.149104798
+ 0.879645943 -1.204362311 0.777877945
+ 0.942477796 -1.280578205 1.633441363
+ 1.005309649 -1.407452145 2.385325060
+ 1.068141502 -1.577565951 3.005551703
+ 1.130973355 -1.781901736 3.471318005
+ 1.193805208 -2.010192036 3.765770485
+ 1.256637061 -2.251314490 3.878644490
+ 1.319468915 -2.493721842 3.806745775
+ 1.382300768 -2.725896717 3.554254889
+ 1.445132621 -2.936819490 3.132835848
+ 1.507964474 -3.116436359 2.561531910
+ 1.570796327 -3.256113784 1.866432816
+ 1.633628180 -3.349064461 1.080099654
+ 1.696460033 -3.390729230 0.240735362
+ 1.759291886 -3.379098611 -0.608908907
+ 1.822123739 -3.314957118 -1.422899114
+ 1.884955592 -3.202033126 -2.153760328
+ 1.947787445 -3.047036792 -2.754397749
+ 2.010619298 -2.859568528 -3.180296191
+ 2.073451151 -2.651880606 -3.391994418
+ 2.136283004 -2.438474843 -3.357827482
+ 2.199114858 -2.235519803 -3.056926751
+ 2.261946711 -2.060071781 -2.482463709
+ 2.324778564 -1.929084752 -1.645119770
+ 2.387610417 -1.858195776 -0.576760378
+ 2.450442270 -1.860273793 0.665712569
+ 2.513274123 -1.943721550 1.996360278
+ 2.576105976 -2.110522417 3.296093502
+ 2.638937829 -2.354026221 4.408485505
+ 2.701769682 -2.656470837 5.135556153
+ 2.764601535 -2.986239274 5.233576852
+ 2.827433388 -3.294855256 4.408951390
+ 2.890265241 -3.513723943 2.314233232
+ 2.953097094 -3.550628422 -1.455654451
+ 3.015928947 -3.285996933 -7.366923892
+ 3.078760801 -2.568960530 -15.950074743
+ 3.141592654 -1.213225986 0.000000000
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/coeffs.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/coeffs.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d61fbc1869fcf3f1a37f7f90b3350fb3ad1aa257
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/coeffs.data.reference
@@ -0,0 +1,231 @@
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 0.000000 0.000000 1
+ 2 0.000000 0.000000 2
+ 3 0.000000 0.000000 3
+ 4 0.000000 0.000000 4
+ 5 0.000000 0.000000 5
+ 6 0.000000 0.000000 6
+ 7 0.000000 0.000000 7
+ 8 0.000000 0.000000 8
+ 9 0.000000 0.000000 9
+ 10 0.000000 0.000000 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -0.525787 -0.525787 1
+ 2 -0.351125 -0.351125 2
+ 3 0.828283 0.828283 3
+ 4 -0.353448 -0.353448 4
+ 5 -0.521257 -0.521257 5
+ 6 0.789277 0.789277 6
+ 7 -0.158744 -0.158744 7
+ 8 -0.644829 -0.644829 8
+ 9 0.698503 0.698503 9
+ 10 0.028687 0.028687 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -0.792749 -1.059711 1
+ 2 -0.507615 -0.664104 2
+ 3 1.236590 1.644897 3
+ 4 -0.557166 -0.760884 4
+ 5 -0.749325 -0.977392 5
+ 6 1.192885 1.596493 6
+ 7 -0.290349 -0.421953 7
+ 8 -0.931763 -1.218696 8
+ 9 1.081302 1.464101 9
+ 10 -0.030418 -0.089523 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -1.045127 -1.549883 1
+ 2 -0.682616 -1.032619 2
+ 3 1.638614 2.442662 3
+ 4 -0.720309 -1.046594 4
+ 5 -1.011653 -1.536311 5
+ 6 1.574762 2.338518 6
+ 7 -0.353298 -0.479196 7
+ 8 -1.257144 -1.907907 8
+ 9 1.415205 2.083011 9
+ 10 0.003520 0.071397 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -1.330163 -2.185271 1
+ 2 -0.789298 -1.109344 2
+ 3 2.020267 3.165225 3
+ 4 -0.976224 -1.743972 4
+ 5 -1.129459 -1.482876 5
+ 6 1.923087 2.968061 6
+ 7 -0.564571 -1.198390 7
+ 8 -1.372417 -1.718236 8
+ 9 1.708161 2.587027 9
+ 10 -0.155676 -0.633266 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -1.623753 -2.798115 1
+ 2 -0.850037 -1.092991 2
+ 3 2.343773 3.637798 3
+ 4 -1.211604 -2.153121 4
+ 5 -1.158470 -1.274513 5
+ 6 2.118632 2.900813 6
+ 7 -0.686806 -1.175746 7
+ 8 -1.415002 -1.585341 8
+ 9 1.790615 2.120433 9
+ 10 -0.147224 -0.113416 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -1.912216 -3.354531 1
+ 2 -0.921691 -1.279964 2
+ 3 2.681598 4.370721 3
+ 4 -1.452223 -2.655322 4
+ 5 -1.209515 -1.464741 5
+ 6 2.360332 3.568829 6
+ 7 -0.839656 -1.603909 7
+ 8 -1.470222 -1.746323 8
+ 9 1.939075 2.681377 9
+ 10 -0.204133 -0.488679 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -2.226247 -4.110430 1
+ 2 -0.880460 -0.633070 2
+ 3 2.758439 3.219490 3
+ 4 -1.516978 -1.905508 4
+ 5 -1.339382 -2.118581 5
+ 6 2.621583 4.189094 6
+ 7 -0.974304 -1.782191 7
+ 8 -1.570203 -2.170090 8
+ 9 2.150213 3.417041 9
+ 10 -0.330495 -1.088667 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -2.549147 -4.809448 1
+ 2 -0.815800 -0.363179 2
+ 3 2.831141 3.340053 3
+ 4 -1.610072 -2.261723 4
+ 5 -1.390981 -1.752179 5
+ 6 2.724934 3.448388 6
+ 7 -1.022203 -1.357498 7
+ 8 -1.699348 -2.603362 8
+ 9 2.328856 3.579357 9
+ 10 -0.388774 -0.796729 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -2.859151 -5.339186 1
+ 2 -0.788219 -0.567571 2
+ 3 2.969667 4.077876 3
+ 4 -1.738899 -2.769515 4
+ 5 -1.455395 -1.970704 5
+ 6 2.884917 4.164779 6
+ 7 -1.110928 -1.820728 7
+ 8 -1.821456 -2.798324 8
+ 9 2.542869 4.254970 9
+ 10 -0.478808 -1.199076 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0.000000 0
+ 1 -3.152772 -5.795358 1
+ 2 -0.797944 -0.885472 2
+ 3 3.154623 4.819228 3
+ 4 -1.872403 -3.073938 4
+ 5 -1.551125 -2.412696 5
+ 6 3.081656 4.852311 6
+ 7 -1.193964 -1.941280 7
+ 8 -1.969951 -3.306403 8
+ 9 2.770339 4.817566 9
+ 10 -0.544576 -1.136489 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/colvar.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/colvar.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..5347163e17e7c85e0d418c312346db4cd151ef3e
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/colvar.data.reference
@@ -0,0 +1,24 @@
+#! FIELDS time phi ves1.bias
+#! SET min_phi -pi
+#! SET max_phi pi
+ 0.000000 -1.238 0.000
+ 1.000000 -1.484 0.000
+ 2.000000 -1.324 0.000
+ 3.000000 -1.334 3.105
+ 4.000000 -1.461 3.077
+ 5.000000 -1.220 4.311
+ 6.000000 -1.388 4.705
+ 7.000000 -1.548 5.843
+ 8.000000 -1.843 3.072
+ 9.000000 -2.242 -2.204
+ 10.000000 -1.148 6.176
+ 11.000000 -1.758 6.322
+ 12.000000 -1.319 8.130
+ 13.000000 -2.991 0.246
+ 14.000000 -1.411 9.430
+ 15.000000 -2.599 -3.544
+ 16.000000 -1.461 10.339
+ 17.000000 -1.379 10.719
+ 18.000000 -1.677 9.805
+ 19.000000 -1.524 11.738
+ 20.000000 -1.200 9.623
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/config b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/config
new file mode 100644
index 0000000000000000000000000000000000000000..d9b022c5f95c12fdf3de7e32807e196863eec343
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/config
@@ -0,0 +1,3 @@
+plumed_modules=ves
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro --dump-forces forces --dump-forces-fmt=%10.6f "
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/fes.ves1.iter-10.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/fes.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f56a8cdde7517497b3777b19ec3a57e1269c85b4
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/fes.ves1.iter-10.data.reference
@@ -0,0 +1,106 @@
+#! FIELDS phi2 ves1.fes
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+ -3.141592654 23.409210496
+ -3.078760801 15.789884780
+ -3.015928947 11.894539193
+ -2.953097094 10.564427375
+ -2.890265241 10.887518693
+ -2.827433388 12.160472158
+ -2.764601535 13.854938123
+ -2.701769682 15.587828182
+ -2.638937829 17.095214511
+ -2.576105976 18.209539974
+ -2.513274123 18.839839628
+ -2.450442270 18.954692879
+ -2.387610417 18.567643399
+ -2.324778564 17.724841098
+ -2.261946711 16.494676945
+ -2.199114858 14.959197213
+ -2.136283004 13.207098890
+ -2.073451151 11.328122467
+ -2.010619298 9.408672192
+ -1.947787445 7.528507067
+ -1.884955592 5.758358525
+ -1.822123739 4.158342689
+ -1.759291886 2.777046569
+ -1.696460033 1.651178401
+ -1.633628180 0.805682609
+ -1.570796327 0.254229625
+ -1.507964474 0.000000000
+ -1.445132621 0.036690926
+ -1.382300768 0.349681465
+ -1.319468915 0.917300457
+ -1.256637061 1.712148260
+ -1.193805208 2.702430238
+ -1.130973355 3.853266122
+ -1.068141502 5.127945242
+ -1.005309649 6.489102994
+ -0.942477796 7.899798871
+ -0.879645943 9.324480974
+ -0.816814090 10.729826075
+ -0.753982237 12.085448101
+ -0.691150384 13.364471342
+ -0.628318531 14.543967741
+ -0.565486678 15.605260382
+ -0.502654825 16.534097668
+ -0.439822972 17.320704791
+ -0.376991118 17.959720869
+ -0.314159265 18.450031630
+ -0.251327412 18.794508744
+ -0.188495559 18.999667863
+ -0.125663706 19.075258129
+ -0.062831853 19.033796395
+ 0.000000000 18.890059645
+ 0.062831853 18.660549128
+ 0.125663706 18.362939569
+ 0.188495559 18.015526472
+ 0.251327412 17.636683995
+ 0.314159265 17.244345220
+ 0.376991118 16.855515802
+ 0.439822972 16.485831008
+ 0.502654825 16.149165120
+ 0.565486678 15.857300933
+ 0.628318531 15.619665848
+ 0.691150384 15.443139652
+ 0.753982237 15.331937684
+ 0.816814090 15.287571574
+ 0.879645943 15.308888210
+ 0.942477796 15.392186046
+ 1.005309649 15.531406268
+ 1.068141502 15.718394770
+ 1.130973355 15.943229300
+ 1.193805208 16.194604610
+ 1.256637061 16.460266902
+ 1.319468915 16.727487434
+ 1.382300768 16.983563691
+ 1.445132621 17.216335251
+ 1.507964474 17.414700181
+ 1.570796327 17.569116693
+ 1.633628180 17.672073729
+ 1.696460033 17.718513257
+ 1.759291886 17.706186274
+ 1.822123739 17.635923920
+ 1.884955592 17.511804628
+ 1.947787445 17.341197981
+ 2.010619298 17.134665867
+ 2.073451151 16.905701617
+ 2.136283004 16.670288178
+ 2.199114858 16.446256933
+ 2.261946711 16.252429558
+ 2.324778564 16.107526433
+ 2.387610417 16.028826388
+ 2.450442270 16.030564225
+ 2.513274123 16.122054351
+ 2.576105976 16.305531079
+ 2.638937829 16.573698662
+ 2.701769682 16.906987054
+ 2.764601535 17.270512529
+ 2.827433388 17.610745939
+ 2.890265241 17.851895281
+ 2.953097094 17.892013617
+ 3.015928947 17.598848084
+ 3.078760801 16.805450904
+ 3.141592654 15.305578844
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/forces.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/forces.reference
new file mode 100644
index 0000000000000000000000000000000000000000..275aba2fab773cb0518961a6ea32bebd24c4eeea
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/forces.reference
@@ -0,0 +1,504 @@
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diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/gradient.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/gradient.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..288a90e877ad11eb86b9123878a387e8eab17247
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/gradient.data.reference
@@ -0,0 +1,210 @@
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.525787 1
+ 2 0.351125 2
+ 3 -0.828283 3
+ 4 0.353448 4
+ 5 0.521257 5
+ 6 -0.789277 6
+ 7 0.158744 7
+ 8 0.644829 8
+ 9 -0.698503 9
+ 10 -0.028687 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.533925 1
+ 2 0.312980 2
+ 3 -0.816615 3
+ 4 0.407436 4
+ 5 0.456136 5
+ 6 -0.807216 6
+ 7 0.263209 7
+ 8 0.573866 8
+ 9 -0.765598 9
+ 10 0.118210 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.490287 1
+ 2 0.368688 2
+ 3 -0.797781 3
+ 4 0.286615 4
+ 5 0.559703 5
+ 6 -0.742599 6
+ 7 0.059013 7
+ 8 0.690263 8
+ 9 -0.621993 9
+ 10 -0.159465 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.636057 1
+ 2 0.078749 2
+ 3 -0.723746 3
+ 4 0.699487 4
+ 5 -0.038780 5
+ 6 -0.637207 6
+ 7 0.720439 7
+ 8 -0.148824 8
+ 9 -0.525136 9
+ 10 0.704087 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.628440 1
+ 2 0.009145 2
+ 3 -0.500710 3
+ 4 0.452066 4
+ 5 -0.114510 5
+ 6 -0.051305 6
+ 7 -0.003267 7
+ 8 -0.036698 8
+ 9 0.329391 9
+ 10 -0.519156 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.559870 1
+ 2 0.189543 2
+ 3 -0.733778 3
+ 4 0.522837 4
+ 5 0.195776 5
+ 6 -0.669627 6
+ 7 0.455943 7
+ 8 0.178436 8
+ 9 -0.561980 9
+ 10 0.371823 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.810739 1
+ 2 -0.546583 2
+ 3 0.330761 3
+ 4 -0.424533 4
+ 5 0.659538 5
+ 6 -0.630820 6
+ 7 0.181117 7
+ 8 0.425211 8
+ 9 -0.735869 9
+ 10 0.625341 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.736230 1
+ 2 -0.300496 2
+ 3 -0.182986 3
+ 4 0.357623 4
+ 5 -0.252738 5
+ 6 0.171620 6
+ 7 -0.283163 7
+ 8 0.433281 8
+ 9 -0.288876 9
+ 10 -0.211460 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.532795 1
+ 2 0.202220 2
+ 3 -0.737949 3
+ 4 0.514688 4
+ 5 0.226495 5
+ 6 -0.716856 6
+ 7 0.473057 7
+ 8 0.239315 8
+ 9 -0.676541 9
+ 10 0.425690 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.gradient index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.000000 0
+ 1 0.460148 1
+ 2 0.316904 2
+ 3 -0.741381 3
+ 4 0.320579 4
+ 5 0.450251 5
+ 6 -0.690447 6
+ 7 0.154251 7
+ 8 0.530856 8
+ 9 -0.588565 9
+ 10 0.003121 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/hessian.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/hessian.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..ae721b7752d48b4241bbc4c44b9949f7954ca211
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/hessian.data.reference
@@ -0,0 +1,220 @@
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.000633 1
+ 2 0.001796 2
+ 3 0.000015 3
+ 4 0.006225 4
+ 5 0.006509 5
+ 6 0.000935 6
+ 7 0.019203 7
+ 8 0.009940 8
+ 9 0.006247 9
+ 10 0.038055 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.000247 1
+ 2 0.000733 2
+ 3 0.000000 3
+ 4 0.002380 4
+ 5 0.002854 5
+ 6 0.000180 6
+ 7 0.007484 7
+ 8 0.004928 8
+ 9 0.001531 9
+ 10 0.015625 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.000430 1
+ 2 0.001112 2
+ 3 0.000042 3
+ 4 0.004447 4
+ 5 0.003437 5
+ 6 0.001423 6
+ 7 0.013449 7
+ 8 0.003667 8
+ 9 0.008056 9
+ 10 0.024610 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.001324 1
+ 2 0.005783 2
+ 3 0.001470 3
+ 4 0.006466 4
+ 5 0.027932 5
+ 6 0.010035 6
+ 7 0.009890 7
+ 8 0.062768 8
+ 9 0.031626 9
+ 10 0.008469 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.018238 1
+ 2 0.079669 2
+ 3 0.024575 3
+ 4 0.055900 4
+ 5 0.265561 5
+ 6 0.113451 6
+ 7 0.030571 7
+ 8 0.278171 8
+ 9 0.156114 9
+ 10 0.001453 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.002941 1
+ 2 0.010578 2
+ 3 0.000661 3
+ 4 0.021917 4
+ 5 0.047810 5
+ 6 0.002059 6
+ 7 0.056817 7
+ 8 0.102463 8
+ 9 0.003140 9
+ 10 0.101758 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.038023 1
+ 2 0.279984 2
+ 3 0.485737 3
+ 4 0.270369 4
+ 5 0.022329 5
+ 6 0.008734 6
+ 7 0.003708 7
+ 8 0.005231 8
+ 9 0.000276 9
+ 10 0.089098 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.019750 1
+ 2 0.123710 2
+ 3 0.135391 3
+ 4 0.003622 4
+ 5 0.145873 5
+ 6 0.363051 6
+ 7 0.175186 7
+ 8 0.000013 8
+ 9 0.099903 9
+ 10 0.106147 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.001353 1
+ 2 0.004800 2
+ 3 0.000248 3
+ 4 0.010582 4
+ 5 0.022065 5
+ 6 0.000644 6
+ 7 0.029309 7
+ 8 0.049062 8
+ 9 0.000742 9
+ 10 0.057220 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.hessian index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+#! SET diagonal_matrix 1
+ 0 0.000000 0
+ 1 0.001603 1
+ 2 0.004519 2
+ 3 0.000026 3
+ 4 0.015677 4
+ 5 0.016027 5
+ 6 0.002278 6
+ 7 0.047477 7
+ 8 0.023317 8
+ 9 0.015168 9
+ 10 0.091228 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/plumed.dat b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..801928845f3add05bb8deb44b5083ce7d2f41fcf
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/plumed.dat
@@ -0,0 +1,51 @@
+# vim:ft=plumed
+
+phi: TORSION ATOMS=5,7,9,15 NOPBC
+phi2: COMBINE ARG=phi PERIODIC=NO
+
+bf1: BF_LEGENDRE ORDER=10 MINIMUM=-pi MAXIMUM=pi SCALED
+td1: TD_WELLTEMPERED BIASFACTOR=10
+
+VES_LINEAR_EXPANSION ...
+ ARG=phi2
+ BASIS_FUNCTIONS=bf1
+ LABEL=ves1
+ TEMP=300.0
+ GRID_BINS=100
+ TARGET_DISTRIBUTION=td1
+... VES_LINEAR_EXPANSION
+
+# NOTE: These parameters do not reflect parameters used in real simulations!
+# This is only for testing!
+#
+
+OPT_AVERAGED_SGD ...
+ BIAS=ves1
+ STRIDE=1000
+ LABEL=o1
+ STEPSIZE=1.0
+ COEFFS_FILE=coeffs.data
+ COEFFS_OUTPUT=1
+ COEFFS_FMT=%12.6f
+ GRADIENT_FILE=gradient.data
+ GRADIENT_OUTPUT=1
+ GRADIENT_FMT=%12.6f
+ HESSIAN_FILE=hessian.data
+ HESSIAN_OUTPUT=1
+ HESSIAN_FMT=%12.6f
+ FES_OUTPUT=10
+ BIAS_OUTPUT=10
+ TARGETDIST_STRIDE=1
+ TARGETDIST_OUTPUT=10
+ TARGETDIST_AVERAGES_OUTPUT=1
+ TARGETDIST_AVERAGES_FMT=%12.6f
+... OPT_AVERAGED_SGD
+
+PRINT ...
+ STRIDE=500
+ ARG=phi,ves1.bias
+ FILE=colvar.data FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist-averages.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist-averages.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..910f01bc04ae6b39610fe11f7da089638df754cd
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist-averages.data.reference
@@ -0,0 +1,231 @@
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 0.000000 1
+ 2 0.000158 2
+ 3 0.000000 3
+ 4 0.000707 4
+ 5 0.000000 5
+ 6 0.001784 6
+ 7 0.000000 7
+ 8 0.003494 8
+ 9 0.000000 9
+ 10 0.005922 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 0.000000 1
+ 2 0.000158 2
+ 3 0.000000 3
+ 4 0.000707 4
+ 5 0.000000 5
+ 6 0.001784 6
+ 7 0.000000 7
+ 8 0.003494 8
+ 9 0.000000 9
+ 10 0.005922 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.010957 1
+ 2 -0.007183 2
+ 3 0.017448 3
+ 4 -0.006746 4
+ 5 -0.010513 5
+ 6 0.017972 6
+ 7 -0.002933 7
+ 8 -0.009944 8
+ 9 0.014832 9
+ 10 0.006142 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.018174 1
+ 2 -0.011409 2
+ 3 0.028417 3
+ 4 -0.012087 4
+ 5 -0.016475 5
+ 6 0.028371 6
+ 7 -0.005966 7
+ 8 -0.017545 8
+ 9 0.024699 9
+ 10 0.004694 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.024920 1
+ 2 -0.015816 2
+ 3 0.038892 3
+ 4 -0.016433 4
+ 5 -0.022869 5
+ 6 0.038021 6
+ 7 -0.007641 7
+ 8 -0.025419 8
+ 9 0.033180 9
+ 10 0.005091 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.032483 1
+ 2 -0.018824 2
+ 3 0.049009 3
+ 4 -0.022883 4
+ 5 -0.026357 5
+ 6 0.047077 6
+ 7 -0.012601 7
+ 8 -0.029092 8
+ 9 0.040854 9
+ 10 0.001335 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.039826 1
+ 2 -0.020793 2
+ 3 0.057620 3
+ 4 -0.028818 4
+ 5 -0.027811 5
+ 6 0.052942 6
+ 7 -0.016068 7
+ 8 -0.030677 8
+ 9 0.044089 9
+ 10 0.000580 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.047374 1
+ 2 -0.022909 2
+ 3 0.066673 3
+ 4 -0.035093 4
+ 5 -0.029526 5
+ 6 0.059632 6
+ 7 -0.020197 7
+ 8 -0.032382 8
+ 9 0.048405 9
+ 10 -0.001366 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.055220 1
+ 2 -0.022762 2
+ 3 0.070536 3
+ 4 -0.037956 4
+ 5 -0.032566 5
+ 6 0.066374 6
+ 7 -0.023836 7
+ 8 -0.035039 8
+ 9 0.053964 9
+ 10 -0.004843 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.062946 1
+ 2 -0.021857 2
+ 3 0.073433 3
+ 4 -0.040655 4
+ 5 -0.034317 5
+ 6 0.070015 6
+ 7 -0.025644 7
+ 8 -0.038225 8
+ 9 0.058821 9
+ 10 -0.007109 10
+#!-------------------
+
+
+#! FIELDS idx_phi2 ves1.targetdist_averages index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi2 11
+ 0 0.707107 0
+ 1 -0.070771 1
+ 2 -0.021659 2
+ 3 0.077894 3
+ 4 -0.044311 4
+ 5 -0.036274 5
+ 6 0.074775 6
+ 7 -0.028279 7
+ 8 -0.041415 8
+ 9 0.064562 9
+ 10 -0.010045 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist.ves1.iter-10.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..521e510d7dc01612e027cf87c2069d00eec30441
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist.ves1.iter-10.data.reference
@@ -0,0 +1,106 @@
+#! FIELDS phi2 targetdist
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+ -3.141592654 0.106233715
+ -3.078760801 0.144186312
+ -3.015928947 0.168556966
+ -2.953097094 0.177789275
+ -2.890265241 0.175501224
+ -2.827433388 0.166769448
+ -2.764601535 0.155816625
+ -2.701769682 0.145359053
+ -2.638937829 0.136834833
+ -2.576105976 0.130856384
+ -2.513274123 0.127591175
+ -2.450442270 0.127005025
+ -2.387610417 0.128991146
+ -2.324778564 0.133424046
+ -2.261946711 0.140169251
+ -2.199114858 0.149068990
+ -2.136283004 0.159916566
+ -2.073451151 0.172428363
+ -2.010619298 0.186220999
+ -1.947787445 0.200800411
+ -1.884955592 0.215568362
+ -1.822123739 0.229849324
+ -1.759291886 0.242936776
+ -1.696460033 0.254153438
+ -1.633628180 0.262916046
+ -1.570796327 0.268793371
+ -1.507964474 0.271546994
+ -1.445132621 0.271147850
+ -1.382300768 0.267766735
+ -1.319468915 0.261742165
+ -1.256637061 0.253532962
+ -1.193805208 0.243664592
+ -1.130973355 0.232677818
+ -1.068141502 0.221086019
+ -1.005309649 0.209344656
+ -0.942477796 0.197833557
+ -0.879645943 0.186850611
+ -0.816814090 0.176614261
+ -0.753982237 0.167271808
+ -0.691150384 0.158910799
+ -0.628318531 0.151571293
+ -0.565486678 0.145257501
+ -0.502654825 0.139947901
+ -0.439822972 0.135603409
+ -0.376991118 0.132173554
+ -0.314159265 0.129600795
+ -0.251327412 0.127823264
+ -0.188495559 0.126776230
+ -0.125663706 0.126392620
+ -0.062831853 0.126602889
+ 0.000000000 0.127334546
+ 0.062831853 0.128511591
+ 0.125663706 0.130054098
+ 0.188495559 0.131878174
+ 0.251327412 0.133896440
+ 0.314159265 0.136019170
+ 0.376991118 0.138156115
+ 0.439822972 0.140218969
+ 0.502654825 0.142124362
+ 0.565486678 0.143797136
+ 0.628318531 0.145173635
+ 0.691150384 0.146204684
+ 0.753982237 0.146857945
+ 0.816814090 0.147119389
+ 0.879645943 0.146993715
+ 0.942477796 0.146503652
+ 1.005309649 0.145688227
+ 1.068141502 0.144600156
+ 1.130973355 0.143302617
+ 1.193805208 0.141865690
+ 1.256637061 0.140362751
+ 1.319468915 0.138867060
+ 1.382300768 0.137448702
+ 1.445132621 0.136171998
+ 1.507964474 0.135093370
+ 1.570796327 0.134259634
+ 1.633628180 0.133706602
+ 1.696460033 0.133457899
+ 1.759291886 0.133523870
+ 1.822123739 0.133900520
+ 1.884955592 0.134568475
+ 1.947787445 0.135492045
+ 2.010619298 0.136618581
+ 2.073451151 0.137878426
+ 2.136283004 0.139185870
+ 2.199114858 0.140441611
+ 2.261946711 0.141537191
+ 2.324778564 0.142361813
+ 2.387610417 0.142811695
+ 2.450442270 0.142801745
+ 2.513274123 0.142278920
+ 2.576105976 0.141236195
+ 2.638937829 0.139725891
+ 2.701769682 0.137871320
+ 2.764601535 0.135876552
+ 2.827433388 0.134035748
+ 2.890265241 0.132746152
+ 2.953097094 0.132532818
+ 3.015928947 0.134099698
+ 3.078760801 0.138433692
+ 3.141592654 0.147013219
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist.ves1.log.iter-10.data.reference b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist.ves1.log.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..dd81a0351bb97eabc5beb163b79f8177619be7ad
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/targetdist.ves1.log.iter-10.data.reference
@@ -0,0 +1,106 @@
+#! FIELDS phi2 log_targetdist
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+ -3.141592654 0.938493684
+ -3.078760801 0.633028916
+ -3.015928947 0.476861443
+ -2.953097094 0.423536213
+ -2.890265241 0.436489198
+ -2.827433388 0.487522905
+ -2.764601535 0.555455380
+ -2.701769682 0.624928307
+ -2.638937829 0.685360612
+ -2.576105976 0.730034798
+ -2.513274123 0.755304007
+ -2.450442270 0.759908565
+ -2.387610417 0.744391446
+ -2.324778564 0.710602838
+ -2.261946711 0.661284588
+ -2.199114858 0.599725997
+ -2.136283004 0.529482995
+ -2.073451151 0.454153351
+ -2.010619298 0.377201078
+ -1.947787445 0.301823777
+ -1.884955592 0.230857128
+ -1.822123739 0.166711233
+ -1.759291886 0.111333984
+ -1.696460033 0.066197042
+ -1.633628180 0.032300450
+ -1.570796327 0.010192266
+ -1.507964474 0.000000000
+ -1.445132621 0.001470968
+ -1.382300768 0.014019005
+ -1.319468915 0.036775298
+ -1.256637061 0.068641372
+ -1.193805208 0.108342556
+ -1.130973355 0.154480473
+ -1.068141502 0.205583363
+ -1.005309649 0.260153249
+ -0.942477796 0.316709158
+ -0.879645943 0.373825785
+ -0.816814090 0.430167177
+ -0.753982237 0.484515132
+ -0.691150384 0.535792181
+ -0.628318531 0.583079120
+ -0.565486678 0.625627178
+ -0.502654825 0.662864996
+ -0.439822972 0.694400695
+ -0.376991118 0.720019353
+ -0.314159265 0.739676298
+ -0.251327412 0.753486656
+ -0.188495559 0.761711647
+ -0.125663706 0.764742120
+ -0.062831853 0.763079887
+ 0.000000000 0.757317367
+ 0.062831853 0.748116110
+ 0.125663706 0.736184708
+ 0.188495559 0.722256644
+ 0.251327412 0.707068550
+ 0.314159265 0.691339380
+ 0.376991118 0.675750902
+ 0.439822972 0.660929948
+ 0.502654825 0.647432747
+ 0.565486678 0.635731682
+ 0.628318531 0.626204705
+ 0.691150384 0.619127630
+ 0.753982237 0.614669456
+ 0.816814090 0.612890784
+ 0.879645943 0.613745384
+ 0.942477796 0.617084860
+ 1.005309649 0.622666308
+ 1.068141502 0.630162825
+ 1.130973355 0.639176618
+ 1.193805208 0.649254452
+ 1.256637061 0.659905063
+ 1.319468915 0.670618144
+ 1.382300768 0.680884443
+ 1.445132621 0.690216438
+ 1.507964474 0.698169045
+ 1.570796327 0.704359724
+ 1.633628180 0.708487353
+ 1.696460033 0.710349150
+ 1.759291886 0.709854952
+ 1.822123739 0.707038078
+ 1.884955592 0.702062038
+ 1.947787445 0.695222283
+ 2.010619298 0.686942248
+ 2.073451151 0.677762891
+ 2.136283004 0.668324981
+ 2.199114858 0.659343392
+ 2.261946711 0.651572700
+ 2.324778564 0.645763420
+ 2.387610417 0.642608273
+ 2.450442270 0.642677944
+ 2.513274123 0.646345855
+ 2.576105976 0.653701582
+ 2.638937829 0.664452631
+ 2.701769682 0.677814425
+ 2.764601535 0.692388448
+ 2.827433388 0.706028673
+ 2.890265241 0.715696540
+ 2.953097094 0.717304916
+ 3.015928947 0.705551679
+ 3.078760801 0.673743761
+ 3.141592654 0.613612709
diff --git a/regtest/ves/rt-le-1d-legendre-scaled-welltempered/traj.gro b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/traj.gro
new file mode 100644
index 0000000000000000000000000000000000000000..c1c387a0144ec8021b9e5b0453be534f2ca906e2
--- /dev/null
+++ b/regtest/ves/rt-le-1d-legendre-scaled-welltempered/traj.gro
@@ -0,0 +1,525 @@
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 0.00000
+ 22
+ 1ACE HH31 1 1.474 1.585 1.200
+ 1ACE CH3 2 1.483 1.508 1.277
+ 1ACE HH32 3 1.476 1.561 1.372
+ 1ACE HH33 4 1.578 1.455 1.278
+ 1ACE C 5 1.353 1.428 1.279
+ 1ACE O 6 1.263 1.449 1.357
+ 2ALA N 7 1.343 1.328 1.191
+ 2ALA H 8 1.415 1.321 1.120
+ 2ALA CA 9 1.233 1.239 1.159
+ 2ALA HA 10 1.144 1.302 1.155
+ 2ALA CB 11 1.244 1.182 1.013
+ 2ALA HB1 12 1.341 1.136 0.992
+ 2ALA HB2 13 1.159 1.117 0.994
+ 2ALA HB3 14 1.242 1.265 0.942
+ 2ALA C 15 1.207 1.140 1.271
+ 2ALA O 16 1.214 1.017 1.241
+ 3NME N 17 1.191 1.177 1.398
+ 3NME H 18 1.192 1.275 1.421
+ 3NME CH3 19 1.189 1.086 1.518
+ 3NME HH31 20 1.170 0.983 1.487
+ 3NME HH32 21 1.283 1.087 1.574
+ 3NME HH33 22 1.108 1.127 1.578
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 1.00000
+ 22
+ 1ACE HH31 1 1.480 1.571 1.214
+ 1ACE CH3 2 1.481 1.493 1.289
+ 1ACE HH32 3 1.502 1.528 1.390
+ 1ACE HH33 4 1.551 1.417 1.255
+ 1ACE C 5 1.344 1.432 1.275
+ 1ACE O 6 1.250 1.462 1.345
+ 2ALA N 7 1.342 1.327 1.193
+ 2ALA H 8 1.430 1.313 1.144
+ 2ALA CA 9 1.233 1.244 1.166
+ 2ALA HA 10 1.144 1.307 1.173
+ 2ALA CB 11 1.240 1.189 1.017
+ 2ALA HB1 12 1.327 1.124 1.000
+ 2ALA HB2 13 1.150 1.128 1.005
+ 2ALA HB3 14 1.251 1.267 0.941
+ 2ALA C 15 1.221 1.133 1.271
+ 2ALA O 16 1.217 1.015 1.238
+ 3NME N 17 1.204 1.174 1.395
+ 3NME H 18 1.200 1.275 1.398
+ 3NME CH3 19 1.188 1.089 1.516
+ 3NME HH31 20 1.083 1.086 1.543
+ 3NME HH32 21 1.233 0.990 1.511
+ 3NME HH33 22 1.241 1.141 1.596
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 2.00000
+ 22
+ 1ACE HH31 1 1.532 1.520 1.209
+ 1ACE CH3 2 1.478 1.493 1.300
+ 1ACE HH32 3 1.465 1.586 1.356
+ 1ACE HH33 4 1.548 1.426 1.350
+ 1ACE C 5 1.352 1.423 1.279
+ 1ACE O 6 1.252 1.461 1.340
+ 2ALA N 7 1.351 1.326 1.190
+ 2ALA H 8 1.442 1.293 1.160
+ 2ALA CA 9 1.232 1.244 1.160
+ 2ALA HA 10 1.146 1.310 1.151
+ 2ALA CB 11 1.241 1.190 1.016
+ 2ALA HB1 12 1.333 1.132 1.008
+ 2ALA HB2 13 1.160 1.123 0.986
+ 2ALA HB3 14 1.242 1.280 0.955
+ 2ALA C 15 1.203 1.138 1.270
+ 2ALA O 16 1.161 1.021 1.240
+ 3NME N 17 1.230 1.171 1.396
+ 3NME H 18 1.257 1.266 1.417
+ 3NME CH3 19 1.217 1.090 1.512
+ 3NME HH31 20 1.144 1.011 1.493
+ 3NME HH32 21 1.307 1.029 1.526
+ 3NME HH33 22 1.212 1.146 1.605
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 3.00000
+ 22
+ 1ACE HH31 1 1.439 1.582 1.175
+ 1ACE CH3 2 1.474 1.516 1.254
+ 1ACE HH32 3 1.480 1.585 1.338
+ 1ACE HH33 4 1.569 1.465 1.242
+ 1ACE C 5 1.364 1.419 1.280
+ 1ACE O 6 1.277 1.446 1.367
+ 2ALA N 7 1.358 1.323 1.194
+ 2ALA H 8 1.443 1.313 1.140
+ 2ALA CA 9 1.235 1.243 1.164
+ 2ALA HA 10 1.150 1.310 1.170
+ 2ALA CB 11 1.240 1.197 1.019
+ 2ALA HB1 12 1.316 1.119 1.016
+ 2ALA HB2 13 1.145 1.157 0.982
+ 2ALA HB3 14 1.279 1.276 0.955
+ 2ALA C 15 1.201 1.137 1.272
+ 2ALA O 16 1.172 1.021 1.232
+ 3NME N 17 1.218 1.166 1.402
+ 3NME H 18 1.240 1.259 1.434
+ 3NME CH3 19 1.186 1.086 1.518
+ 3NME HH31 20 1.225 0.984 1.527
+ 3NME HH32 21 1.193 1.134 1.616
+ 3NME HH33 22 1.081 1.058 1.509
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 4.00000
+ 22
+ 1ACE HH31 1 1.549 1.508 1.196
+ 1ACE CH3 2 1.500 1.486 1.290
+ 1ACE HH32 3 1.487 1.571 1.357
+ 1ACE HH33 4 1.563 1.415 1.343
+ 1ACE C 5 1.362 1.425 1.270
+ 1ACE O 6 1.265 1.465 1.340
+ 2ALA N 7 1.349 1.324 1.182
+ 2ALA H 8 1.432 1.287 1.138
+ 2ALA CA 9 1.221 1.249 1.168
+ 2ALA HA 10 1.138 1.318 1.184
+ 2ALA CB 11 1.201 1.194 1.025
+ 2ALA HB1 12 1.276 1.117 1.005
+ 2ALA HB2 13 1.096 1.165 1.014
+ 2ALA HB3 14 1.229 1.265 0.947
+ 2ALA C 15 1.217 1.141 1.275
+ 2ALA O 16 1.234 1.024 1.243
+ 3NME N 17 1.183 1.174 1.400
+ 3NME H 18 1.184 1.274 1.412
+ 3NME CH3 19 1.187 1.078 1.509
+ 3NME HH31 20 1.248 0.990 1.490
+ 3NME HH32 21 1.220 1.120 1.604
+ 3NME HH33 22 1.088 1.035 1.527
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 5.00000
+ 22
+ 1ACE HH31 1 1.449 1.585 1.168
+ 1ACE CH3 2 1.479 1.518 1.248
+ 1ACE HH32 3 1.523 1.577 1.328
+ 1ACE HH33 4 1.565 1.461 1.213
+ 1ACE C 5 1.364 1.422 1.284
+ 1ACE O 6 1.305 1.438 1.389
+ 2ALA N 7 1.347 1.326 1.187
+ 2ALA H 8 1.423 1.328 1.122
+ 2ALA CA 9 1.226 1.241 1.162
+ 2ALA HA 10 1.139 1.308 1.162
+ 2ALA CB 11 1.236 1.193 1.023
+ 2ALA HB1 12 1.314 1.117 1.012
+ 2ALA HB2 13 1.137 1.167 0.986
+ 2ALA HB3 14 1.273 1.278 0.966
+ 2ALA C 15 1.195 1.133 1.268
+ 2ALA O 16 1.173 1.016 1.239
+ 3NME N 17 1.204 1.175 1.393
+ 3NME H 18 1.211 1.275 1.403
+ 3NME CH3 19 1.188 1.090 1.513
+ 3NME HH31 20 1.089 1.044 1.509
+ 3NME HH32 21 1.267 1.014 1.509
+ 3NME HH33 22 1.189 1.145 1.607
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 6.00000
+ 22
+ 1ACE HH31 1 1.517 1.511 1.181
+ 1ACE CH3 2 1.490 1.488 1.284
+ 1ACE HH32 3 1.482 1.582 1.339
+ 1ACE HH33 4 1.569 1.421 1.316
+ 1ACE C 5 1.359 1.414 1.282
+ 1ACE O 6 1.272 1.447 1.358
+ 2ALA N 7 1.351 1.320 1.186
+ 2ALA H 8 1.434 1.297 1.133
+ 2ALA CA 9 1.220 1.251 1.159
+ 2ALA HA 10 1.139 1.323 1.167
+ 2ALA CB 11 1.220 1.194 1.018
+ 2ALA HB1 12 1.298 1.120 1.003
+ 2ALA HB2 13 1.120 1.158 0.994
+ 2ALA HB3 14 1.224 1.286 0.960
+ 2ALA C 15 1.201 1.139 1.270
+ 2ALA O 16 1.190 1.022 1.239
+ 3NME N 17 1.203 1.178 1.393
+ 3NME H 18 1.207 1.277 1.409
+ 3NME CH3 19 1.211 1.102 1.515
+ 3NME HH31 20 1.111 1.064 1.534
+ 3NME HH32 21 1.275 1.017 1.492
+ 3NME HH33 22 1.264 1.151 1.597
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 7.00000
+ 22
+ 1ACE HH31 1 1.483 1.590 1.185
+ 1ACE CH3 2 1.505 1.501 1.245
+ 1ACE HH32 3 1.538 1.533 1.344
+ 1ACE HH33 4 1.580 1.430 1.209
+ 1ACE C 5 1.379 1.418 1.267
+ 1ACE O 6 1.298 1.443 1.349
+ 2ALA N 7 1.360 1.320 1.187
+ 2ALA H 8 1.426 1.297 1.114
+ 2ALA CA 9 1.224 1.253 1.180
+ 2ALA HA 10 1.147 1.326 1.205
+ 2ALA CB 11 1.174 1.215 1.037
+ 2ALA HB1 12 1.245 1.152 0.983
+ 2ALA HB2 13 1.084 1.154 1.032
+ 2ALA HB3 14 1.153 1.311 0.992
+ 2ALA C 15 1.212 1.141 1.280
+ 2ALA O 16 1.219 1.022 1.244
+ 3NME N 17 1.191 1.176 1.408
+ 3NME H 18 1.207 1.275 1.423
+ 3NME CH3 19 1.162 1.068 1.509
+ 3NME HH31 20 1.229 0.982 1.503
+ 3NME HH32 21 1.162 1.109 1.610
+ 3NME HH33 22 1.056 1.044 1.499
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 8.00000
+ 22
+ 1ACE HH31 1 1.576 1.425 1.169
+ 1ACE CH3 2 1.523 1.455 1.260
+ 1ACE HH32 3 1.547 1.556 1.294
+ 1ACE HH33 4 1.566 1.393 1.338
+ 1ACE C 5 1.385 1.422 1.255
+ 1ACE O 6 1.308 1.499 1.305
+ 2ALA N 7 1.346 1.311 1.189
+ 2ALA H 8 1.419 1.248 1.159
+ 2ALA CA 9 1.210 1.260 1.193
+ 2ALA HA 10 1.139 1.326 1.242
+ 2ALA CB 11 1.152 1.252 1.051
+ 2ALA HB1 12 1.230 1.210 0.987
+ 2ALA HB2 13 1.066 1.185 1.052
+ 2ALA HB3 14 1.127 1.354 1.024
+ 2ALA C 15 1.206 1.136 1.282
+ 2ALA O 16 1.195 1.023 1.229
+ 3NME N 17 1.210 1.152 1.420
+ 3NME H 18 1.221 1.243 1.463
+ 3NME CH3 19 1.185 1.048 1.518
+ 3NME HH31 20 1.195 0.948 1.475
+ 3NME HH32 21 1.261 1.070 1.593
+ 3NME HH33 22 1.088 1.064 1.565
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 9.00000
+ 22
+ 1ACE HH31 1 1.515 1.474 1.040
+ 1ACE CH3 2 1.535 1.461 1.147
+ 1ACE HH32 3 1.561 1.560 1.184
+ 1ACE HH33 4 1.612 1.386 1.165
+ 1ACE C 5 1.406 1.430 1.217
+ 1ACE O 6 1.361 1.502 1.307
+ 2ALA N 7 1.345 1.316 1.190
+ 2ALA H 8 1.384 1.254 1.121
+ 2ALA CA 9 1.217 1.277 1.242
+ 2ALA HA 10 1.187 1.348 1.319
+ 2ALA CB 11 1.111 1.278 1.134
+ 2ALA HB1 12 1.129 1.198 1.062
+ 2ALA HB2 13 1.018 1.269 1.189
+ 2ALA HB3 14 1.121 1.372 1.079
+ 2ALA C 15 1.217 1.133 1.309
+ 2ALA O 16 1.293 1.044 1.265
+ 3NME N 17 1.132 1.116 1.408
+ 3NME H 18 1.076 1.195 1.437
+ 3NME CH3 19 1.112 1.003 1.490
+ 3NME HH31 20 1.156 0.910 1.456
+ 3NME HH32 21 1.153 1.026 1.588
+ 3NME HH33 22 1.005 0.985 1.500
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 10.00000
+ 22
+ 1ACE HH31 1 1.536 1.485 1.135
+ 1ACE CH3 2 1.521 1.460 1.240
+ 1ACE HH32 3 1.528 1.557 1.289
+ 1ACE HH33 4 1.602 1.397 1.276
+ 1ACE C 5 1.385 1.401 1.261
+ 1ACE O 6 1.341 1.416 1.373
+ 2ALA N 7 1.322 1.332 1.167
+ 2ALA H 8 1.364 1.316 1.076
+ 2ALA CA 9 1.190 1.273 1.177
+ 2ALA HA 10 1.125 1.352 1.216
+ 2ALA CB 11 1.134 1.230 1.038
+ 2ALA HB1 12 1.167 1.128 1.016
+ 2ALA HB2 13 1.026 1.238 1.046
+ 2ALA HB3 14 1.174 1.287 0.953
+ 2ALA C 15 1.183 1.157 1.283
+ 2ALA O 16 1.111 1.061 1.259
+ 3NME N 17 1.264 1.157 1.396
+ 3NME H 18 1.320 1.241 1.405
+ 3NME CH3 19 1.264 1.070 1.510
+ 3NME HH31 20 1.163 1.057 1.548
+ 3NME HH32 21 1.311 0.974 1.487
+ 3NME HH33 22 1.326 1.109 1.592
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 11.00000
+ 22
+ 1ACE HH31 1 1.607 1.359 1.178
+ 1ACE CH3 2 1.535 1.442 1.176
+ 1ACE HH32 3 1.521 1.470 1.072
+ 1ACE HH33 4 1.569 1.533 1.224
+ 1ACE C 5 1.402 1.412 1.242
+ 1ACE O 6 1.368 1.454 1.350
+ 2ALA N 7 1.319 1.332 1.177
+ 2ALA H 8 1.363 1.279 1.103
+ 2ALA CA 9 1.194 1.289 1.231
+ 2ALA HA 10 1.153 1.355 1.308
+ 2ALA CB 11 1.092 1.300 1.113
+ 2ALA HB1 12 1.137 1.243 1.032
+ 2ALA HB2 13 1.001 1.243 1.131
+ 2ALA HB3 14 1.070 1.405 1.095
+ 2ALA C 15 1.198 1.143 1.290
+ 2ALA O 16 1.237 1.057 1.213
+ 3NME N 17 1.171 1.126 1.422
+ 3NME H 18 1.164 1.213 1.472
+ 3NME CH3 19 1.200 1.009 1.496
+ 3NME HH31 20 1.118 0.938 1.493
+ 3NME HH32 21 1.284 0.953 1.454
+ 3NME HH33 22 1.230 1.031 1.598
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 12.00000
+ 22
+ 1ACE HH31 1 1.491 1.569 1.138
+ 1ACE CH3 2 1.511 1.462 1.134
+ 1ACE HH32 3 1.614 1.449 1.166
+ 1ACE HH33 4 1.495 1.444 1.028
+ 1ACE C 5 1.416 1.394 1.229
+ 1ACE O 6 1.445 1.392 1.345
+ 2ALA N 7 1.299 1.357 1.181
+ 2ALA H 8 1.278 1.358 1.082
+ 2ALA CA 9 1.196 1.301 1.267
+ 2ALA HA 10 1.185 1.364 1.355
+ 2ALA CB 11 1.063 1.319 1.182
+ 2ALA HB1 12 1.057 1.248 1.100
+ 2ALA HB2 13 0.976 1.288 1.240
+ 2ALA HB3 14 1.037 1.423 1.161
+ 2ALA C 15 1.226 1.161 1.304
+ 2ALA O 16 1.317 1.094 1.258
+ 3NME N 17 1.135 1.110 1.387
+ 3NME H 18 1.064 1.174 1.419
+ 3NME CH3 19 1.121 0.972 1.429
+ 3NME HH31 20 1.163 0.900 1.358
+ 3NME HH32 21 1.177 0.954 1.520
+ 3NME HH33 22 1.016 0.942 1.428
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 13.00000
+ 22
+ 1ACE HH31 1 1.528 1.537 1.077
+ 1ACE CH3 2 1.543 1.448 1.137
+ 1ACE HH32 3 1.634 1.463 1.195
+ 1ACE HH33 4 1.560 1.362 1.072
+ 1ACE C 5 1.421 1.428 1.229
+ 1ACE O 6 1.396 1.520 1.301
+ 2ALA N 7 1.355 1.314 1.219
+ 2ALA H 8 1.385 1.241 1.156
+ 2ALA CA 9 1.249 1.276 1.311
+ 2ALA HA 10 1.297 1.288 1.409
+ 2ALA CB 11 1.122 1.359 1.284
+ 2ALA HB1 12 1.072 1.325 1.193
+ 2ALA HB2 13 1.053 1.352 1.367
+ 2ALA HB3 14 1.153 1.463 1.275
+ 2ALA C 15 1.204 1.131 1.290
+ 2ALA O 16 1.225 1.070 1.185
+ 3NME N 17 1.131 1.077 1.382
+ 3NME H 18 1.104 1.132 1.463
+ 3NME CH3 19 1.083 0.939 1.380
+ 3NME HH31 20 1.012 0.925 1.298
+ 3NME HH32 21 1.168 0.871 1.372
+ 3NME HH33 22 1.036 0.915 1.475
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 14.00000
+ 22
+ 1ACE HH31 1 1.543 1.468 1.123
+ 1ACE CH3 2 1.548 1.443 1.229
+ 1ACE HH32 3 1.566 1.540 1.276
+ 1ACE HH33 4 1.634 1.382 1.257
+ 1ACE C 5 1.420 1.385 1.285
+ 1ACE O 6 1.412 1.375 1.404
+ 2ALA N 7 1.324 1.361 1.200
+ 2ALA H 8 1.345 1.354 1.101
+ 2ALA CA 9 1.189 1.323 1.244
+ 2ALA HA 10 1.163 1.394 1.323
+ 2ALA CB 11 1.094 1.344 1.125
+ 2ALA HB1 12 1.098 1.270 1.045
+ 2ALA HB2 13 0.995 1.352 1.170
+ 2ALA HB3 14 1.120 1.440 1.079
+ 2ALA C 15 1.166 1.169 1.284
+ 2ALA O 16 1.055 1.145 1.330
+ 3NME N 17 1.263 1.077 1.279
+ 3NME H 18 1.356 1.102 1.247
+ 3NME CH3 19 1.246 0.942 1.335
+ 3NME HH31 20 1.142 0.911 1.345
+ 3NME HH32 21 1.293 0.868 1.270
+ 3NME HH33 22 1.292 0.934 1.434
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 15.00000
+ 22
+ 1ACE HH31 1 1.508 1.417 1.043
+ 1ACE CH3 2 1.539 1.448 1.143
+ 1ACE HH32 3 1.565 1.553 1.146
+ 1ACE HH33 4 1.630 1.395 1.169
+ 1ACE C 5 1.438 1.410 1.253
+ 1ACE O 6 1.429 1.471 1.356
+ 2ALA N 7 1.348 1.327 1.217
+ 2ALA H 8 1.362 1.285 1.126
+ 2ALA CA 9 1.233 1.289 1.298
+ 2ALA HA 10 1.269 1.295 1.401
+ 2ALA CB 11 1.107 1.379 1.286
+ 2ALA HB1 12 1.057 1.360 1.191
+ 2ALA HB2 13 1.034 1.369 1.366
+ 2ALA HB3 14 1.141 1.482 1.282
+ 2ALA C 15 1.192 1.141 1.266
+ 2ALA O 16 1.220 1.089 1.156
+ 3NME N 17 1.131 1.075 1.364
+ 3NME H 18 1.117 1.126 1.450
+ 3NME CH3 19 1.090 0.931 1.376
+ 3NME HH31 20 1.156 0.880 1.446
+ 3NME HH32 21 0.996 0.929 1.431
+ 3NME HH33 22 1.090 0.874 1.283
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 16.00000
+ 22
+ 1ACE HH31 1 1.587 1.386 1.166
+ 1ACE CH3 2 1.554 1.425 1.262
+ 1ACE HH32 3 1.559 1.534 1.266
+ 1ACE HH33 4 1.627 1.390 1.335
+ 1ACE C 5 1.417 1.372 1.300
+ 1ACE O 6 1.390 1.364 1.421
+ 2ALA N 7 1.334 1.344 1.205
+ 2ALA H 8 1.365 1.367 1.111
+ 2ALA CA 9 1.190 1.324 1.235
+ 2ALA HA 10 1.160 1.386 1.319
+ 2ALA CB 11 1.105 1.363 1.112
+ 2ALA HB1 12 1.129 1.297 1.029
+ 2ALA HB2 13 0.999 1.351 1.131
+ 2ALA HB3 14 1.125 1.467 1.088
+ 2ALA C 15 1.162 1.180 1.282
+ 2ALA O 16 1.054 1.128 1.258
+ 3NME N 17 1.261 1.106 1.318
+ 3NME H 18 1.349 1.152 1.336
+ 3NME CH3 19 1.250 0.960 1.324
+ 3NME HH31 20 1.264 0.908 1.229
+ 3NME HH32 21 1.322 0.926 1.399
+ 3NME HH33 22 1.153 0.923 1.357
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 17.00000
+ 22
+ 1ACE HH31 1 1.614 1.382 1.173
+ 1ACE CH3 2 1.559 1.432 1.253
+ 1ACE HH32 3 1.547 1.532 1.213
+ 1ACE HH33 4 1.625 1.444 1.339
+ 1ACE C 5 1.426 1.380 1.288
+ 1ACE O 6 1.411 1.348 1.406
+ 2ALA N 7 1.325 1.370 1.200
+ 2ALA H 8 1.341 1.388 1.102
+ 2ALA CA 9 1.189 1.318 1.239
+ 2ALA HA 10 1.170 1.358 1.338
+ 2ALA CB 11 1.084 1.388 1.158
+ 2ALA HB1 12 1.113 1.369 1.055
+ 2ALA HB2 13 0.994 1.336 1.189
+ 2ALA HB3 14 1.075 1.493 1.186
+ 2ALA C 15 1.170 1.163 1.252
+ 2ALA O 16 1.097 1.103 1.171
+ 3NME N 17 1.235 1.099 1.349
+ 3NME H 18 1.305 1.153 1.399
+ 3NME CH3 19 1.220 0.964 1.393
+ 3NME HH31 20 1.315 0.912 1.406
+ 3NME HH32 21 1.168 0.953 1.489
+ 3NME HH33 22 1.178 0.897 1.318
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 18.00000
+ 22
+ 1ACE HH31 1 1.555 1.419 1.126
+ 1ACE CH3 2 1.554 1.431 1.235
+ 1ACE HH32 3 1.554 1.535 1.267
+ 1ACE HH33 4 1.638 1.381 1.283
+ 1ACE C 5 1.423 1.378 1.292
+ 1ACE O 6 1.416 1.347 1.409
+ 2ALA N 7 1.322 1.351 1.211
+ 2ALA H 8 1.350 1.370 1.115
+ 2ALA CA 9 1.185 1.318 1.251
+ 2ALA HA 10 1.171 1.358 1.352
+ 2ALA CB 11 1.091 1.400 1.149
+ 2ALA HB1 12 1.059 1.346 1.060
+ 2ALA HB2 13 1.008 1.443 1.205
+ 2ALA HB3 14 1.154 1.480 1.109
+ 2ALA C 15 1.163 1.166 1.255
+ 2ALA O 16 1.060 1.108 1.214
+ 3NME N 17 1.255 1.102 1.328
+ 3NME H 18 1.335 1.159 1.354
+ 3NME CH3 19 1.246 0.964 1.369
+ 3NME HH31 20 1.154 0.913 1.344
+ 3NME HH32 21 1.323 0.899 1.327
+ 3NME HH33 22 1.251 0.953 1.477
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 19.00000
+ 22
+ 1ACE HH31 1 1.559 1.326 1.133
+ 1ACE CH3 2 1.552 1.413 1.200
+ 1ACE HH32 3 1.538 1.504 1.142
+ 1ACE HH33 4 1.631 1.428 1.273
+ 1ACE C 5 1.426 1.375 1.280
+ 1ACE O 6 1.428 1.345 1.398
+ 2ALA N 7 1.319 1.363 1.209
+ 2ALA H 8 1.322 1.382 1.110
+ 2ALA CA 9 1.191 1.329 1.265
+ 2ALA HA 10 1.186 1.364 1.368
+ 2ALA CB 11 1.075 1.391 1.178
+ 2ALA HB1 12 1.098 1.383 1.072
+ 2ALA HB2 13 0.980 1.348 1.211
+ 2ALA HB3 14 1.066 1.499 1.192
+ 2ALA C 15 1.169 1.174 1.275
+ 2ALA O 16 1.086 1.118 1.203
+ 3NME N 17 1.233 1.105 1.363
+ 3NME H 18 1.312 1.150 1.405
+ 3NME CH3 19 1.242 0.956 1.350
+ 3NME HH31 20 1.219 0.899 1.440
+ 3NME HH32 21 1.165 0.918 1.284
+ 3NME HH33 22 1.333 0.921 1.301
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 20.00000
+ 22
+ 1ACE HH31 1 1.622 1.459 1.287
+ 1ACE CH3 2 1.546 1.434 1.214
+ 1ACE HH32 3 1.578 1.365 1.135
+ 1ACE HH33 4 1.509 1.531 1.180
+ 1ACE C 5 1.430 1.358 1.283
+ 1ACE O 6 1.444 1.310 1.394
+ 2ALA N 7 1.315 1.370 1.215
+ 2ALA H 8 1.323 1.427 1.132
+ 2ALA CA 9 1.178 1.334 1.258
+ 2ALA HA 10 1.163 1.376 1.357
+ 2ALA CB 11 1.079 1.393 1.158
+ 2ALA HB1 12 1.096 1.348 1.060
+ 2ALA HB2 13 0.979 1.367 1.192
+ 2ALA HB3 14 1.087 1.501 1.165
+ 2ALA C 15 1.163 1.177 1.270
+ 2ALA O 16 1.073 1.114 1.216
+ 3NME N 17 1.249 1.110 1.347
+ 3NME H 18 1.324 1.165 1.388
+ 3NME CH3 19 1.242 0.964 1.360
+ 3NME HH31 20 1.325 0.920 1.416
+ 3NME HH32 21 1.151 0.938 1.414
+ 3NME HH33 22 1.221 0.913 1.266
+ 10.00000 10.00000 10.00000
diff --git a/regtest/ves/rt-le-2d-fesproj/Makefile b/regtest/ves/rt-le-2d-fesproj/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/ves/rt-le-2d-fesproj/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/ves/rt-le-2d-fesproj/config b/regtest/ves/rt-le-2d-fesproj/config
new file mode 100644
index 0000000000000000000000000000000000000000..6ed5446ca530c1f5b039fad96d74b39b3a46e357
--- /dev/null
+++ b/regtest/ves/rt-le-2d-fesproj/config
@@ -0,0 +1,3 @@
+plumed_modules=ves
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro "
diff --git a/regtest/ves/rt-le-2d-fesproj/fes.ves1.proj-1.iter-10.data.reference b/regtest/ves/rt-le-2d-fesproj/fes.ves1.proj-1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..79b33461b4b565bfca7eeb22834332b2e2aeac29
--- /dev/null
+++ b/regtest/ves/rt-le-2d-fesproj/fes.ves1.proj-1.iter-10.data.reference
@@ -0,0 +1,105 @@
+#! FIELDS phi projection
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET nbins_phi 100
+#! SET periodic_phi true
+ -3.141592654 66.393226598
+ -3.078760801 65.086904472
+ -3.015928947 63.680652835
+ -2.953097094 62.305399037
+ -2.890265241 61.128931230
+ -2.827433388 60.328099405
+ -2.764601535 60.043574974
+ -2.701769682 60.325582888
+ -2.638937829 61.080556881
+ -2.576105976 62.062985544
+ -2.513274123 63.007546316
+ -2.450442270 63.820350256
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+ -2.324778564 65.205498116
+ -2.261946711 65.759476125
+ -2.199114858 66.099310665
+ -2.136283004 66.005646215
+ -2.073451151 64.919127911
+ -2.010619298 61.794839211
+ -1.947787445 56.390614291
+ -1.884955592 49.521374308
+ -1.822123739 41.776758894
+ -1.759291886 33.566119636
+ -1.696460033 25.321210819
+ -1.633628180 17.520570795
+ -1.570796327 10.659111989
+ -1.507964474 5.204837445
+ -1.445132621 1.555275238
+ -1.382300768 0.000000000
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+ -1.256637061 3.637309894
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+ 0.188495559 62.588073058
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+ 0.314159265 65.813542493
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+ 0.439822972 68.580241000
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+ 0.942477796 66.683836331
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+ 1.130973355 64.015985387
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+ 1.319468915 64.392937866
+ 1.382300768 65.316028229
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+ 1.507964474 67.539914376
+ 1.570796327 68.461694627
+ 1.633628180 69.101929821
+ 1.696460033 69.449240068
+ 1.759291886 69.530994409
+ 1.822123739 69.376699651
+ 1.884955592 69.007270642
+ 1.947787445 68.437890318
+ 2.010619298 67.686731865
+ 2.073451151 66.789899771
+ 2.136283004 65.819591580
+ 2.199114858 64.891734693
+ 2.261946711 64.150104526
+ 2.324778564 63.732326202
+ 2.387610417 63.735031845
+ 2.450442270 64.188635820
+ 2.513274123 65.042328085
+ 2.576105976 66.159110458
+ 2.638937829 67.330918341
+ 2.701769682 68.334888091
+ 2.764601535 69.019754297
+ 2.827433388 69.343492984
+ 2.890265241 69.327988549
+ 2.953097094 69.003653084
+ 3.015928947 68.392007169
+ 3.078760801 67.512198235
diff --git a/regtest/ves/rt-le-2d-fesproj/fes.ves1.proj-2.iter-10.data.reference b/regtest/ves/rt-le-2d-fesproj/fes.ves1.proj-2.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..5d9c6210af09d81746d6014ca8b9faf89700ce60
--- /dev/null
+++ b/regtest/ves/rt-le-2d-fesproj/fes.ves1.proj-2.iter-10.data.reference
@@ -0,0 +1,125 @@
+#! FIELDS psi projection
+#! SET min_psi -pi
+#! SET max_psi pi
+#! SET nbins_psi 120
+#! SET periodic_psi true
+ -3.141592654 59.746188051
+ -3.089232776 60.524940378
+ -3.036872898 61.283572847
+ -2.984513021 61.987358810
+ -2.932153143 62.606629927
+ -2.879793266 63.119069444
+ -2.827433388 63.511415112
+ -2.775073511 63.780201880
+ -2.722713633 63.931386651
+ -2.670353756 63.978965310
+ -2.617993878 63.942883569
+ -2.565634000 63.846607727
+ -2.513274123 63.714691812
+ -2.460914245 63.570604889
+ -2.408554368 63.434999615
+ -2.356194490 63.324528308
+ -2.303834613 63.251252731
+ -2.251474735 63.222642498
+ -2.199114858 63.242097958
+ -2.146754980 63.309853795
+ -2.094395102 63.424028264
+ -2.042035225 63.581521341
+ -1.989675347 63.778490128
+ -1.937315470 64.010269389
+ -1.884955592 64.270817200
+ -1.832595715 64.551952526
+ -1.780235837 64.842724593
+ -1.727875959 65.129190853
+ -1.675516082 65.394726107
+ -1.623156204 65.620819825
+ -1.570796327 65.788226512
+ -1.518436449 65.878374917
+ -1.466076572 65.875094288
+ -1.413716694 65.766824045
+ -1.361356817 65.549297876
+ -1.308996939 65.228152855
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+ 1.308996939 17.687739086
+ 1.361356817 21.968561575
+ 1.413716694 26.411282848
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+ 1.518436449 35.396192166
+ 1.570796327 39.759013853
+ 1.623156204 43.929323086
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+ 2.827433388 56.654587897
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+ 2.984513021 57.661719646
+ 3.036872898 58.277870947
+ 3.089232776 58.984635494
diff --git a/regtest/ves/rt-le-2d-fesproj/plumed.dat b/regtest/ves/rt-le-2d-fesproj/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..e72888b75d10d76285ee982c832905dbcc6fa1a2
--- /dev/null
+++ b/regtest/ves/rt-le-2d-fesproj/plumed.dat
@@ -0,0 +1,35 @@
+# vim:ft=plumed
+
+# To test if projected fes file is outputted if the full fes file is not. Based on rt-le-2d-uniform.
+
+phi: TORSION ATOMS=5,7,9,15 NOPBC
+psi: TORSION ATOMS=7,9,15,17 NOPBC
+
+bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
+bf2: BF_FOURIER ORDER=4 MINIMUM=-pi MAXIMUM=pi
+
+VES_LINEAR_EXPANSION ...
+ ARG=phi,psi
+ BASIS_FUNCTIONS=bf1,bf2
+ LABEL=ves1
+ TEMP=300.0
+ GRID_BINS=100,120
+ PROJ_ARG1=phi
+ PROJ_ARG2=psi
+... VES_LINEAR_EXPANSION
+
+# NOTE: These parameters do not reflect parameters used in real simulations!
+# This is only for testing!
+#
+
+OPT_AVERAGED_SGD ...
+ BIAS=ves1
+ STRIDE=1000
+ LABEL=o1
+ STEPSIZE=1.0
+ FES_PROJ_OUTPUT=10
+ TARGETDIST_AVERAGES_FMT=%12.6f
+... OPT_AVERAGED_SGD
+
+ENDPLUMED
+
diff --git a/regtest/ves/rt-le-2d-fesproj/traj.gro b/regtest/ves/rt-le-2d-fesproj/traj.gro
new file mode 100644
index 0000000000000000000000000000000000000000..c1c387a0144ec8021b9e5b0453be534f2ca906e2
--- /dev/null
+++ b/regtest/ves/rt-le-2d-fesproj/traj.gro
@@ -0,0 +1,525 @@
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 0.00000
+ 22
+ 1ACE HH31 1 1.474 1.585 1.200
+ 1ACE CH3 2 1.483 1.508 1.277
+ 1ACE HH32 3 1.476 1.561 1.372
+ 1ACE HH33 4 1.578 1.455 1.278
+ 1ACE C 5 1.353 1.428 1.279
+ 1ACE O 6 1.263 1.449 1.357
+ 2ALA N 7 1.343 1.328 1.191
+ 2ALA H 8 1.415 1.321 1.120
+ 2ALA CA 9 1.233 1.239 1.159
+ 2ALA HA 10 1.144 1.302 1.155
+ 2ALA CB 11 1.244 1.182 1.013
+ 2ALA HB1 12 1.341 1.136 0.992
+ 2ALA HB2 13 1.159 1.117 0.994
+ 2ALA HB3 14 1.242 1.265 0.942
+ 2ALA C 15 1.207 1.140 1.271
+ 2ALA O 16 1.214 1.017 1.241
+ 3NME N 17 1.191 1.177 1.398
+ 3NME H 18 1.192 1.275 1.421
+ 3NME CH3 19 1.189 1.086 1.518
+ 3NME HH31 20 1.170 0.983 1.487
+ 3NME HH32 21 1.283 1.087 1.574
+ 3NME HH33 22 1.108 1.127 1.578
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 1.00000
+ 22
+ 1ACE HH31 1 1.480 1.571 1.214
+ 1ACE CH3 2 1.481 1.493 1.289
+ 1ACE HH32 3 1.502 1.528 1.390
+ 1ACE HH33 4 1.551 1.417 1.255
+ 1ACE C 5 1.344 1.432 1.275
+ 1ACE O 6 1.250 1.462 1.345
+ 2ALA N 7 1.342 1.327 1.193
+ 2ALA H 8 1.430 1.313 1.144
+ 2ALA CA 9 1.233 1.244 1.166
+ 2ALA HA 10 1.144 1.307 1.173
+ 2ALA CB 11 1.240 1.189 1.017
+ 2ALA HB1 12 1.327 1.124 1.000
+ 2ALA HB2 13 1.150 1.128 1.005
+ 2ALA HB3 14 1.251 1.267 0.941
+ 2ALA C 15 1.221 1.133 1.271
+ 2ALA O 16 1.217 1.015 1.238
+ 3NME N 17 1.204 1.174 1.395
+ 3NME H 18 1.200 1.275 1.398
+ 3NME CH3 19 1.188 1.089 1.516
+ 3NME HH31 20 1.083 1.086 1.543
+ 3NME HH32 21 1.233 0.990 1.511
+ 3NME HH33 22 1.241 1.141 1.596
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 2.00000
+ 22
+ 1ACE HH31 1 1.532 1.520 1.209
+ 1ACE CH3 2 1.478 1.493 1.300
+ 1ACE HH32 3 1.465 1.586 1.356
+ 1ACE HH33 4 1.548 1.426 1.350
+ 1ACE C 5 1.352 1.423 1.279
+ 1ACE O 6 1.252 1.461 1.340
+ 2ALA N 7 1.351 1.326 1.190
+ 2ALA H 8 1.442 1.293 1.160
+ 2ALA CA 9 1.232 1.244 1.160
+ 2ALA HA 10 1.146 1.310 1.151
+ 2ALA CB 11 1.241 1.190 1.016
+ 2ALA HB1 12 1.333 1.132 1.008
+ 2ALA HB2 13 1.160 1.123 0.986
+ 2ALA HB3 14 1.242 1.280 0.955
+ 2ALA C 15 1.203 1.138 1.270
+ 2ALA O 16 1.161 1.021 1.240
+ 3NME N 17 1.230 1.171 1.396
+ 3NME H 18 1.257 1.266 1.417
+ 3NME CH3 19 1.217 1.090 1.512
+ 3NME HH31 20 1.144 1.011 1.493
+ 3NME HH32 21 1.307 1.029 1.526
+ 3NME HH33 22 1.212 1.146 1.605
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 3.00000
+ 22
+ 1ACE HH31 1 1.439 1.582 1.175
+ 1ACE CH3 2 1.474 1.516 1.254
+ 1ACE HH32 3 1.480 1.585 1.338
+ 1ACE HH33 4 1.569 1.465 1.242
+ 1ACE C 5 1.364 1.419 1.280
+ 1ACE O 6 1.277 1.446 1.367
+ 2ALA N 7 1.358 1.323 1.194
+ 2ALA H 8 1.443 1.313 1.140
+ 2ALA CA 9 1.235 1.243 1.164
+ 2ALA HA 10 1.150 1.310 1.170
+ 2ALA CB 11 1.240 1.197 1.019
+ 2ALA HB1 12 1.316 1.119 1.016
+ 2ALA HB2 13 1.145 1.157 0.982
+ 2ALA HB3 14 1.279 1.276 0.955
+ 2ALA C 15 1.201 1.137 1.272
+ 2ALA O 16 1.172 1.021 1.232
+ 3NME N 17 1.218 1.166 1.402
+ 3NME H 18 1.240 1.259 1.434
+ 3NME CH3 19 1.186 1.086 1.518
+ 3NME HH31 20 1.225 0.984 1.527
+ 3NME HH32 21 1.193 1.134 1.616
+ 3NME HH33 22 1.081 1.058 1.509
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 4.00000
+ 22
+ 1ACE HH31 1 1.549 1.508 1.196
+ 1ACE CH3 2 1.500 1.486 1.290
+ 1ACE HH32 3 1.487 1.571 1.357
+ 1ACE HH33 4 1.563 1.415 1.343
+ 1ACE C 5 1.362 1.425 1.270
+ 1ACE O 6 1.265 1.465 1.340
+ 2ALA N 7 1.349 1.324 1.182
+ 2ALA H 8 1.432 1.287 1.138
+ 2ALA CA 9 1.221 1.249 1.168
+ 2ALA HA 10 1.138 1.318 1.184
+ 2ALA CB 11 1.201 1.194 1.025
+ 2ALA HB1 12 1.276 1.117 1.005
+ 2ALA HB2 13 1.096 1.165 1.014
+ 2ALA HB3 14 1.229 1.265 0.947
+ 2ALA C 15 1.217 1.141 1.275
+ 2ALA O 16 1.234 1.024 1.243
+ 3NME N 17 1.183 1.174 1.400
+ 3NME H 18 1.184 1.274 1.412
+ 3NME CH3 19 1.187 1.078 1.509
+ 3NME HH31 20 1.248 0.990 1.490
+ 3NME HH32 21 1.220 1.120 1.604
+ 3NME HH33 22 1.088 1.035 1.527
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 5.00000
+ 22
+ 1ACE HH31 1 1.449 1.585 1.168
+ 1ACE CH3 2 1.479 1.518 1.248
+ 1ACE HH32 3 1.523 1.577 1.328
+ 1ACE HH33 4 1.565 1.461 1.213
+ 1ACE C 5 1.364 1.422 1.284
+ 1ACE O 6 1.305 1.438 1.389
+ 2ALA N 7 1.347 1.326 1.187
+ 2ALA H 8 1.423 1.328 1.122
+ 2ALA CA 9 1.226 1.241 1.162
+ 2ALA HA 10 1.139 1.308 1.162
+ 2ALA CB 11 1.236 1.193 1.023
+ 2ALA HB1 12 1.314 1.117 1.012
+ 2ALA HB2 13 1.137 1.167 0.986
+ 2ALA HB3 14 1.273 1.278 0.966
+ 2ALA C 15 1.195 1.133 1.268
+ 2ALA O 16 1.173 1.016 1.239
+ 3NME N 17 1.204 1.175 1.393
+ 3NME H 18 1.211 1.275 1.403
+ 3NME CH3 19 1.188 1.090 1.513
+ 3NME HH31 20 1.089 1.044 1.509
+ 3NME HH32 21 1.267 1.014 1.509
+ 3NME HH33 22 1.189 1.145 1.607
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 6.00000
+ 22
+ 1ACE HH31 1 1.517 1.511 1.181
+ 1ACE CH3 2 1.490 1.488 1.284
+ 1ACE HH32 3 1.482 1.582 1.339
+ 1ACE HH33 4 1.569 1.421 1.316
+ 1ACE C 5 1.359 1.414 1.282
+ 1ACE O 6 1.272 1.447 1.358
+ 2ALA N 7 1.351 1.320 1.186
+ 2ALA H 8 1.434 1.297 1.133
+ 2ALA CA 9 1.220 1.251 1.159
+ 2ALA HA 10 1.139 1.323 1.167
+ 2ALA CB 11 1.220 1.194 1.018
+ 2ALA HB1 12 1.298 1.120 1.003
+ 2ALA HB2 13 1.120 1.158 0.994
+ 2ALA HB3 14 1.224 1.286 0.960
+ 2ALA C 15 1.201 1.139 1.270
+ 2ALA O 16 1.190 1.022 1.239
+ 3NME N 17 1.203 1.178 1.393
+ 3NME H 18 1.207 1.277 1.409
+ 3NME CH3 19 1.211 1.102 1.515
+ 3NME HH31 20 1.111 1.064 1.534
+ 3NME HH32 21 1.275 1.017 1.492
+ 3NME HH33 22 1.264 1.151 1.597
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 7.00000
+ 22
+ 1ACE HH31 1 1.483 1.590 1.185
+ 1ACE CH3 2 1.505 1.501 1.245
+ 1ACE HH32 3 1.538 1.533 1.344
+ 1ACE HH33 4 1.580 1.430 1.209
+ 1ACE C 5 1.379 1.418 1.267
+ 1ACE O 6 1.298 1.443 1.349
+ 2ALA N 7 1.360 1.320 1.187
+ 2ALA H 8 1.426 1.297 1.114
+ 2ALA CA 9 1.224 1.253 1.180
+ 2ALA HA 10 1.147 1.326 1.205
+ 2ALA CB 11 1.174 1.215 1.037
+ 2ALA HB1 12 1.245 1.152 0.983
+ 2ALA HB2 13 1.084 1.154 1.032
+ 2ALA HB3 14 1.153 1.311 0.992
+ 2ALA C 15 1.212 1.141 1.280
+ 2ALA O 16 1.219 1.022 1.244
+ 3NME N 17 1.191 1.176 1.408
+ 3NME H 18 1.207 1.275 1.423
+ 3NME CH3 19 1.162 1.068 1.509
+ 3NME HH31 20 1.229 0.982 1.503
+ 3NME HH32 21 1.162 1.109 1.610
+ 3NME HH33 22 1.056 1.044 1.499
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 8.00000
+ 22
+ 1ACE HH31 1 1.576 1.425 1.169
+ 1ACE CH3 2 1.523 1.455 1.260
+ 1ACE HH32 3 1.547 1.556 1.294
+ 1ACE HH33 4 1.566 1.393 1.338
+ 1ACE C 5 1.385 1.422 1.255
+ 1ACE O 6 1.308 1.499 1.305
+ 2ALA N 7 1.346 1.311 1.189
+ 2ALA H 8 1.419 1.248 1.159
+ 2ALA CA 9 1.210 1.260 1.193
+ 2ALA HA 10 1.139 1.326 1.242
+ 2ALA CB 11 1.152 1.252 1.051
+ 2ALA HB1 12 1.230 1.210 0.987
+ 2ALA HB2 13 1.066 1.185 1.052
+ 2ALA HB3 14 1.127 1.354 1.024
+ 2ALA C 15 1.206 1.136 1.282
+ 2ALA O 16 1.195 1.023 1.229
+ 3NME N 17 1.210 1.152 1.420
+ 3NME H 18 1.221 1.243 1.463
+ 3NME CH3 19 1.185 1.048 1.518
+ 3NME HH31 20 1.195 0.948 1.475
+ 3NME HH32 21 1.261 1.070 1.593
+ 3NME HH33 22 1.088 1.064 1.565
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 9.00000
+ 22
+ 1ACE HH31 1 1.515 1.474 1.040
+ 1ACE CH3 2 1.535 1.461 1.147
+ 1ACE HH32 3 1.561 1.560 1.184
+ 1ACE HH33 4 1.612 1.386 1.165
+ 1ACE C 5 1.406 1.430 1.217
+ 1ACE O 6 1.361 1.502 1.307
+ 2ALA N 7 1.345 1.316 1.190
+ 2ALA H 8 1.384 1.254 1.121
+ 2ALA CA 9 1.217 1.277 1.242
+ 2ALA HA 10 1.187 1.348 1.319
+ 2ALA CB 11 1.111 1.278 1.134
+ 2ALA HB1 12 1.129 1.198 1.062
+ 2ALA HB2 13 1.018 1.269 1.189
+ 2ALA HB3 14 1.121 1.372 1.079
+ 2ALA C 15 1.217 1.133 1.309
+ 2ALA O 16 1.293 1.044 1.265
+ 3NME N 17 1.132 1.116 1.408
+ 3NME H 18 1.076 1.195 1.437
+ 3NME CH3 19 1.112 1.003 1.490
+ 3NME HH31 20 1.156 0.910 1.456
+ 3NME HH32 21 1.153 1.026 1.588
+ 3NME HH33 22 1.005 0.985 1.500
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 10.00000
+ 22
+ 1ACE HH31 1 1.536 1.485 1.135
+ 1ACE CH3 2 1.521 1.460 1.240
+ 1ACE HH32 3 1.528 1.557 1.289
+ 1ACE HH33 4 1.602 1.397 1.276
+ 1ACE C 5 1.385 1.401 1.261
+ 1ACE O 6 1.341 1.416 1.373
+ 2ALA N 7 1.322 1.332 1.167
+ 2ALA H 8 1.364 1.316 1.076
+ 2ALA CA 9 1.190 1.273 1.177
+ 2ALA HA 10 1.125 1.352 1.216
+ 2ALA CB 11 1.134 1.230 1.038
+ 2ALA HB1 12 1.167 1.128 1.016
+ 2ALA HB2 13 1.026 1.238 1.046
+ 2ALA HB3 14 1.174 1.287 0.953
+ 2ALA C 15 1.183 1.157 1.283
+ 2ALA O 16 1.111 1.061 1.259
+ 3NME N 17 1.264 1.157 1.396
+ 3NME H 18 1.320 1.241 1.405
+ 3NME CH3 19 1.264 1.070 1.510
+ 3NME HH31 20 1.163 1.057 1.548
+ 3NME HH32 21 1.311 0.974 1.487
+ 3NME HH33 22 1.326 1.109 1.592
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 11.00000
+ 22
+ 1ACE HH31 1 1.607 1.359 1.178
+ 1ACE CH3 2 1.535 1.442 1.176
+ 1ACE HH32 3 1.521 1.470 1.072
+ 1ACE HH33 4 1.569 1.533 1.224
+ 1ACE C 5 1.402 1.412 1.242
+ 1ACE O 6 1.368 1.454 1.350
+ 2ALA N 7 1.319 1.332 1.177
+ 2ALA H 8 1.363 1.279 1.103
+ 2ALA CA 9 1.194 1.289 1.231
+ 2ALA HA 10 1.153 1.355 1.308
+ 2ALA CB 11 1.092 1.300 1.113
+ 2ALA HB1 12 1.137 1.243 1.032
+ 2ALA HB2 13 1.001 1.243 1.131
+ 2ALA HB3 14 1.070 1.405 1.095
+ 2ALA C 15 1.198 1.143 1.290
+ 2ALA O 16 1.237 1.057 1.213
+ 3NME N 17 1.171 1.126 1.422
+ 3NME H 18 1.164 1.213 1.472
+ 3NME CH3 19 1.200 1.009 1.496
+ 3NME HH31 20 1.118 0.938 1.493
+ 3NME HH32 21 1.284 0.953 1.454
+ 3NME HH33 22 1.230 1.031 1.598
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 12.00000
+ 22
+ 1ACE HH31 1 1.491 1.569 1.138
+ 1ACE CH3 2 1.511 1.462 1.134
+ 1ACE HH32 3 1.614 1.449 1.166
+ 1ACE HH33 4 1.495 1.444 1.028
+ 1ACE C 5 1.416 1.394 1.229
+ 1ACE O 6 1.445 1.392 1.345
+ 2ALA N 7 1.299 1.357 1.181
+ 2ALA H 8 1.278 1.358 1.082
+ 2ALA CA 9 1.196 1.301 1.267
+ 2ALA HA 10 1.185 1.364 1.355
+ 2ALA CB 11 1.063 1.319 1.182
+ 2ALA HB1 12 1.057 1.248 1.100
+ 2ALA HB2 13 0.976 1.288 1.240
+ 2ALA HB3 14 1.037 1.423 1.161
+ 2ALA C 15 1.226 1.161 1.304
+ 2ALA O 16 1.317 1.094 1.258
+ 3NME N 17 1.135 1.110 1.387
+ 3NME H 18 1.064 1.174 1.419
+ 3NME CH3 19 1.121 0.972 1.429
+ 3NME HH31 20 1.163 0.900 1.358
+ 3NME HH32 21 1.177 0.954 1.520
+ 3NME HH33 22 1.016 0.942 1.428
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 13.00000
+ 22
+ 1ACE HH31 1 1.528 1.537 1.077
+ 1ACE CH3 2 1.543 1.448 1.137
+ 1ACE HH32 3 1.634 1.463 1.195
+ 1ACE HH33 4 1.560 1.362 1.072
+ 1ACE C 5 1.421 1.428 1.229
+ 1ACE O 6 1.396 1.520 1.301
+ 2ALA N 7 1.355 1.314 1.219
+ 2ALA H 8 1.385 1.241 1.156
+ 2ALA CA 9 1.249 1.276 1.311
+ 2ALA HA 10 1.297 1.288 1.409
+ 2ALA CB 11 1.122 1.359 1.284
+ 2ALA HB1 12 1.072 1.325 1.193
+ 2ALA HB2 13 1.053 1.352 1.367
+ 2ALA HB3 14 1.153 1.463 1.275
+ 2ALA C 15 1.204 1.131 1.290
+ 2ALA O 16 1.225 1.070 1.185
+ 3NME N 17 1.131 1.077 1.382
+ 3NME H 18 1.104 1.132 1.463
+ 3NME CH3 19 1.083 0.939 1.380
+ 3NME HH31 20 1.012 0.925 1.298
+ 3NME HH32 21 1.168 0.871 1.372
+ 3NME HH33 22 1.036 0.915 1.475
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 14.00000
+ 22
+ 1ACE HH31 1 1.543 1.468 1.123
+ 1ACE CH3 2 1.548 1.443 1.229
+ 1ACE HH32 3 1.566 1.540 1.276
+ 1ACE HH33 4 1.634 1.382 1.257
+ 1ACE C 5 1.420 1.385 1.285
+ 1ACE O 6 1.412 1.375 1.404
+ 2ALA N 7 1.324 1.361 1.200
+ 2ALA H 8 1.345 1.354 1.101
+ 2ALA CA 9 1.189 1.323 1.244
+ 2ALA HA 10 1.163 1.394 1.323
+ 2ALA CB 11 1.094 1.344 1.125
+ 2ALA HB1 12 1.098 1.270 1.045
+ 2ALA HB2 13 0.995 1.352 1.170
+ 2ALA HB3 14 1.120 1.440 1.079
+ 2ALA C 15 1.166 1.169 1.284
+ 2ALA O 16 1.055 1.145 1.330
+ 3NME N 17 1.263 1.077 1.279
+ 3NME H 18 1.356 1.102 1.247
+ 3NME CH3 19 1.246 0.942 1.335
+ 3NME HH31 20 1.142 0.911 1.345
+ 3NME HH32 21 1.293 0.868 1.270
+ 3NME HH33 22 1.292 0.934 1.434
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 15.00000
+ 22
+ 1ACE HH31 1 1.508 1.417 1.043
+ 1ACE CH3 2 1.539 1.448 1.143
+ 1ACE HH32 3 1.565 1.553 1.146
+ 1ACE HH33 4 1.630 1.395 1.169
+ 1ACE C 5 1.438 1.410 1.253
+ 1ACE O 6 1.429 1.471 1.356
+ 2ALA N 7 1.348 1.327 1.217
+ 2ALA H 8 1.362 1.285 1.126
+ 2ALA CA 9 1.233 1.289 1.298
+ 2ALA HA 10 1.269 1.295 1.401
+ 2ALA CB 11 1.107 1.379 1.286
+ 2ALA HB1 12 1.057 1.360 1.191
+ 2ALA HB2 13 1.034 1.369 1.366
+ 2ALA HB3 14 1.141 1.482 1.282
+ 2ALA C 15 1.192 1.141 1.266
+ 2ALA O 16 1.220 1.089 1.156
+ 3NME N 17 1.131 1.075 1.364
+ 3NME H 18 1.117 1.126 1.450
+ 3NME CH3 19 1.090 0.931 1.376
+ 3NME HH31 20 1.156 0.880 1.446
+ 3NME HH32 21 0.996 0.929 1.431
+ 3NME HH33 22 1.090 0.874 1.283
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 16.00000
+ 22
+ 1ACE HH31 1 1.587 1.386 1.166
+ 1ACE CH3 2 1.554 1.425 1.262
+ 1ACE HH32 3 1.559 1.534 1.266
+ 1ACE HH33 4 1.627 1.390 1.335
+ 1ACE C 5 1.417 1.372 1.300
+ 1ACE O 6 1.390 1.364 1.421
+ 2ALA N 7 1.334 1.344 1.205
+ 2ALA H 8 1.365 1.367 1.111
+ 2ALA CA 9 1.190 1.324 1.235
+ 2ALA HA 10 1.160 1.386 1.319
+ 2ALA CB 11 1.105 1.363 1.112
+ 2ALA HB1 12 1.129 1.297 1.029
+ 2ALA HB2 13 0.999 1.351 1.131
+ 2ALA HB3 14 1.125 1.467 1.088
+ 2ALA C 15 1.162 1.180 1.282
+ 2ALA O 16 1.054 1.128 1.258
+ 3NME N 17 1.261 1.106 1.318
+ 3NME H 18 1.349 1.152 1.336
+ 3NME CH3 19 1.250 0.960 1.324
+ 3NME HH31 20 1.264 0.908 1.229
+ 3NME HH32 21 1.322 0.926 1.399
+ 3NME HH33 22 1.153 0.923 1.357
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 17.00000
+ 22
+ 1ACE HH31 1 1.614 1.382 1.173
+ 1ACE CH3 2 1.559 1.432 1.253
+ 1ACE HH32 3 1.547 1.532 1.213
+ 1ACE HH33 4 1.625 1.444 1.339
+ 1ACE C 5 1.426 1.380 1.288
+ 1ACE O 6 1.411 1.348 1.406
+ 2ALA N 7 1.325 1.370 1.200
+ 2ALA H 8 1.341 1.388 1.102
+ 2ALA CA 9 1.189 1.318 1.239
+ 2ALA HA 10 1.170 1.358 1.338
+ 2ALA CB 11 1.084 1.388 1.158
+ 2ALA HB1 12 1.113 1.369 1.055
+ 2ALA HB2 13 0.994 1.336 1.189
+ 2ALA HB3 14 1.075 1.493 1.186
+ 2ALA C 15 1.170 1.163 1.252
+ 2ALA O 16 1.097 1.103 1.171
+ 3NME N 17 1.235 1.099 1.349
+ 3NME H 18 1.305 1.153 1.399
+ 3NME CH3 19 1.220 0.964 1.393
+ 3NME HH31 20 1.315 0.912 1.406
+ 3NME HH32 21 1.168 0.953 1.489
+ 3NME HH33 22 1.178 0.897 1.318
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 18.00000
+ 22
+ 1ACE HH31 1 1.555 1.419 1.126
+ 1ACE CH3 2 1.554 1.431 1.235
+ 1ACE HH32 3 1.554 1.535 1.267
+ 1ACE HH33 4 1.638 1.381 1.283
+ 1ACE C 5 1.423 1.378 1.292
+ 1ACE O 6 1.416 1.347 1.409
+ 2ALA N 7 1.322 1.351 1.211
+ 2ALA H 8 1.350 1.370 1.115
+ 2ALA CA 9 1.185 1.318 1.251
+ 2ALA HA 10 1.171 1.358 1.352
+ 2ALA CB 11 1.091 1.400 1.149
+ 2ALA HB1 12 1.059 1.346 1.060
+ 2ALA HB2 13 1.008 1.443 1.205
+ 2ALA HB3 14 1.154 1.480 1.109
+ 2ALA C 15 1.163 1.166 1.255
+ 2ALA O 16 1.060 1.108 1.214
+ 3NME N 17 1.255 1.102 1.328
+ 3NME H 18 1.335 1.159 1.354
+ 3NME CH3 19 1.246 0.964 1.369
+ 3NME HH31 20 1.154 0.913 1.344
+ 3NME HH32 21 1.323 0.899 1.327
+ 3NME HH33 22 1.251 0.953 1.477
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 19.00000
+ 22
+ 1ACE HH31 1 1.559 1.326 1.133
+ 1ACE CH3 2 1.552 1.413 1.200
+ 1ACE HH32 3 1.538 1.504 1.142
+ 1ACE HH33 4 1.631 1.428 1.273
+ 1ACE C 5 1.426 1.375 1.280
+ 1ACE O 6 1.428 1.345 1.398
+ 2ALA N 7 1.319 1.363 1.209
+ 2ALA H 8 1.322 1.382 1.110
+ 2ALA CA 9 1.191 1.329 1.265
+ 2ALA HA 10 1.186 1.364 1.368
+ 2ALA CB 11 1.075 1.391 1.178
+ 2ALA HB1 12 1.098 1.383 1.072
+ 2ALA HB2 13 0.980 1.348 1.211
+ 2ALA HB3 14 1.066 1.499 1.192
+ 2ALA C 15 1.169 1.174 1.275
+ 2ALA O 16 1.086 1.118 1.203
+ 3NME N 17 1.233 1.105 1.363
+ 3NME H 18 1.312 1.150 1.405
+ 3NME CH3 19 1.242 0.956 1.350
+ 3NME HH31 20 1.219 0.899 1.440
+ 3NME HH32 21 1.165 0.918 1.284
+ 3NME HH33 22 1.333 0.921 1.301
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 20.00000
+ 22
+ 1ACE HH31 1 1.622 1.459 1.287
+ 1ACE CH3 2 1.546 1.434 1.214
+ 1ACE HH32 3 1.578 1.365 1.135
+ 1ACE HH33 4 1.509 1.531 1.180
+ 1ACE C 5 1.430 1.358 1.283
+ 1ACE O 6 1.444 1.310 1.394
+ 2ALA N 7 1.315 1.370 1.215
+ 2ALA H 8 1.323 1.427 1.132
+ 2ALA CA 9 1.178 1.334 1.258
+ 2ALA HA 10 1.163 1.376 1.357
+ 2ALA CB 11 1.079 1.393 1.158
+ 2ALA HB1 12 1.096 1.348 1.060
+ 2ALA HB2 13 0.979 1.367 1.192
+ 2ALA HB3 14 1.087 1.501 1.165
+ 2ALA C 15 1.163 1.177 1.270
+ 2ALA O 16 1.073 1.114 1.216
+ 3NME N 17 1.249 1.110 1.347
+ 3NME H 18 1.324 1.165 1.388
+ 3NME CH3 19 1.242 0.964 1.360
+ 3NME HH31 20 1.325 0.920 1.416
+ 3NME HH32 21 1.151 0.938 1.414
+ 3NME HH33 22 1.221 0.913 1.266
+ 10.00000 10.00000 10.00000
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/Makefile b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/bias.ves1.iter-10.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/bias.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..afbfb8beb4a19b775d2ad01e90e801e1df8e510d
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/bias.ves1.iter-10.data.reference
@@ -0,0 +1,10310 @@
+#! FIELDS phi2 psi2 ves1.bias der_phi2 der_psi2
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+#! SET min_psi2 -pi
+#! SET max_psi2 pi
+#! SET nbins_psi2 101
+#! SET periodic_psi2 false
+ -3.141592654 -3.141592654 -1.701899815 63.859397761 -0.005586975
+ -3.078760801 -3.141592654 -4.587341632 30.137947056 -40.563311706
+ -3.015928947 -3.141592654 -5.727040801 7.793498129 -57.497050645
+ -2.953097094 -3.141592654 -5.747660282 -5.894789568 -59.134962513
+ -2.890265241 -3.141592654 -5.120377143 -13.166501776 -51.767329465
+ -2.827433388 -3.141592654 -4.189086042 -15.843661705 -40.012005491
+ -2.764601535 -3.141592654 -3.194798401 -15.388205212 -27.131032959
+ -2.701769682 -3.141592654 -2.296614387 -12.953666252 -15.303230463
+ -2.638937829 -3.141592654 -1.589618543 -9.431481346 -5.857222659
+ -2.576105976 -3.141592654 -1.120024802 -5.492303554 0.530934991
+ -2.513274123 -3.141592654 -0.897872644 -1.622698605 3.671687238
+ -2.450442270 -3.141592654 -0.907553301 1.842421654 3.723906044
+ -2.387610417 -3.141592654 -1.116423126 4.691290376 1.081529700
+ -2.324778564 -3.141592654 -1.481740530 6.810379981 -3.718107261
+ -2.261946711 -3.141592654 -1.956143220 8.162794453 -10.067025167
+ -2.199114858 -3.141592654 -2.491863778 8.769670436 -17.342966369
+ -2.136283004 -3.141592654 -3.043863946 8.694313416 -24.951689221
+ -2.073451151 -3.141592654 -3.572051295 8.028810406 -32.357287380
+ -2.010619298 -3.141592654 -4.042726103 6.882875273 -39.102432604
+ -1.947787445 -3.141592654 -4.429391468 5.374697179 -44.820250331
+ -1.884955592 -3.141592654 -4.713045668 3.623576585 -49.239359662
+ -1.822123739 -3.141592654 -4.882062649 1.744146800 -52.183442625
+ -1.759291886 -3.141592654 -4.931754284 -0.158007757 -53.566551392
+ -1.696460033 -3.141592654 -4.863696559 -1.989512651 -53.385216271
+ -1.633628180 -3.141592654 -4.684891164 -3.671307535 -51.708281317
+ -1.570796327 -3.141592654 -4.406824088 -5.139844943 -48.665268222
+ -1.507964474 -3.141592654 -4.044473641 -6.347523840 -44.433952200
+ -1.445132621 -3.141592654 -3.615311868 -7.262486758 -39.227725758
+ -1.382300768 -3.141592654 -3.138335586 -7.867898563 -33.283227169
+ -1.319468915 -3.141592654 -2.633156182 -8.160814397 -26.848619765
+ -1.256637061 -3.141592654 -2.119170868 -8.150734366 -20.172825670
+ -1.193805208 -3.141592654 -1.614832259 -7.857932826 -13.495942875
+ -1.130973355 -3.141592654 -1.137027928 -7.311640901 -7.041007356
+ -1.068141502 -3.141592654 -0.700576922 -6.548151945 -1.007201954
+ -1.005309649 -3.141592654 -0.317846105 -5.608911229 4.435439344
+ -0.942477796 -3.141592654 0.001514387 -4.538642989 9.149829594
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diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/coeffs.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/coeffs.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..7cf4dd1af318a9336a1a266d981a6e497061e360
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/coeffs.data.reference
@@ -0,0 +1,1210 @@
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+ 7 6 -0.638630 -1.151122 73
+ 8 6 -0.535525 -0.681074 74
+ 9 6 1.099717 1.574110 75
+ 10 6 -0.668248 -1.112542 76
+ 0 7 -1.042428 -1.705963 77
+ 1 7 0.937883 1.847934 78
+ 2 7 0.116179 -0.526916 79
+ 3 7 -0.721999 -0.472815 80
+ 4 7 0.288227 0.364483 81
+ 5 7 0.499726 0.240675 82
+ 6 7 -0.605360 -0.369891 83
+ 7 7 -0.160216 -0.384542 84
+ 8 7 0.762032 0.885894 85
+ 9 7 -0.452013 -0.491274 86
+ 10 7 -0.491366 -0.537823 87
+ 0 8 -1.020411 -1.412824 88
+ 1 8 0.993849 1.685690 89
+ 2 8 -0.077857 -0.934854 90
+ 3 8 -0.599055 0.155896 91
+ 4 8 0.418209 0.158875 92
+ 5 8 0.352270 0.174206 93
+ 6 8 -0.752196 -0.407619 94
+ 7 8 0.342033 0.181068 95
+ 8 8 0.416145 0.354231 96
+ 9 8 -0.732293 -0.730159 97
+ 10 8 0.300513 0.545838 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.coeffs ves1.aux_coeffs index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.000000 0.000000 0
+ 1 0 -2.277420 -4.221962 1
+ 2 0 -0.597062 -0.692359 2
+ 3 0 2.397958 3.812936 3
+ 4 0 -1.406611 -2.374430 4
+ 5 0 -1.156973 -1.840584 5
+ 6 0 2.308540 3.773073 6
+ 7 0 -0.882580 -1.485796 7
+ 8 0 -1.460356 -2.481501 8
+ 9 0 2.048166 3.609226 9
+ 10 0 -0.404957 -0.884692 10
+ 0 1 1.826590 3.393546 11
+ 1 1 -1.685663 -3.239206 12
+ 2 1 0.031430 0.484139 13
+ 3 1 1.222792 1.714115 14
+ 4 1 -0.874890 -1.333569 15
+ 5 1 -0.486214 -0.770576 16
+ 6 1 1.269591 1.971460 17
+ 7 1 -0.626119 -0.880354 18
+ 8 1 -0.684179 -1.330185 19
+ 9 1 1.143476 2.084041 20
+ 10 1 -0.384055 -0.716808 21
+ 0 2 -0.900067 -1.214768 22
+ 1 2 0.436962 0.369733 23
+ 2 2 1.158133 2.304681 24
+ 3 2 -1.825322 -3.349388 25
+ 4 2 0.770189 1.533819 26
+ 5 2 0.967735 1.466373 27
+ 6 2 -1.556554 -2.694542 28
+ 7 2 0.420699 1.031071 29
+ 8 2 1.078418 1.428144 30
+ 9 2 -1.288944 -2.027792 31
+ 10 2 -0.011432 0.141163 32
+ 0 3 -1.334176 -1.895128 33
+ 1 3 0.916079 1.141308 34
+ 2 3 1.020158 1.945413 35
+ 3 3 -2.092550 -3.609577 36
+ 4 3 1.269570 2.283054 37
+ 5 3 0.742054 1.014533 38
+ 6 3 -1.700487 -2.711567 39
+ 7 3 0.877209 1.622040 40
+ 8 3 0.842921 1.072259 41
+ 9 3 -1.435023 -2.153052 42
+ 10 3 0.394452 0.686555 43
+ 0 4 0.628486 1.219448 44
+ 1 4 -0.443219 -0.952735 45
+ 2 4 -0.289009 -0.349667 46
+ 3 4 0.453227 0.697433 47
+ 4 4 0.194002 0.350680 48
+ 5 4 -1.011468 -1.851626 49
+ 6 4 0.802111 1.557386 50
+ 7 4 0.285178 0.320583 51
+ 8 4 -1.128350 -1.940187 52
+ 9 4 0.747220 1.476818 53
+ 10 4 0.383106 0.363509 54
+ 0 5 1.806677 2.912500 55
+ 1 5 -1.283746 -2.036418 56
+ 2 5 -1.117520 -1.904538 57
+ 3 5 2.184878 3.604783 58
+ 4 5 -0.761340 -1.222987 59
+ 5 5 -1.812318 -3.110827 60
+ 6 5 2.415480 4.195155 61
+ 7 5 -0.535412 -1.133244 62
+ 8 5 -1.939895 -3.039017 63
+ 9 5 2.172163 3.671068 64
+ 10 5 -0.163447 -0.554461 65
+ 0 6 0.642616 0.910496 66
+ 1 6 -0.364170 -0.327939 67
+ 2 6 -0.622857 -1.326584 68
+ 3 6 1.112636 1.983254 69
+ 4 6 -0.498502 -0.762023 70
+ 5 6 -0.720731 -1.444593 71
+ 6 6 1.269213 2.303367 72
+ 7 6 -0.704817 -1.300499 73
+ 8 6 -0.575758 -0.937854 74
+ 9 6 1.184146 1.944010 75
+ 10 6 -0.720804 -1.193807 76
+ 0 7 -1.128079 -1.898934 77
+ 1 7 1.041591 1.974965 78
+ 2 7 0.065576 -0.389844 79
+ 3 7 -0.721621 -0.718218 80
+ 4 7 0.301049 0.416441 81
+ 5 7 0.494306 0.445526 82
+ 6 7 -0.602765 -0.579410 83
+ 7 7 -0.186692 -0.424975 84
+ 8 7 0.797785 1.119569 85
+ 9 7 -0.469897 -0.630858 86
+ 10 7 -0.508662 -0.664328 87
+ 0 8 -1.110365 -1.919948 88
+ 1 8 1.100733 2.062697 89
+ 2 8 -0.138818 -0.687468 90
+ 3 8 -0.582856 -0.437066 91
+ 4 8 0.419285 0.428972 92
+ 5 8 0.369272 0.522296 93
+ 6 8 -0.773225 -0.962482 94
+ 7 8 0.340304 0.324741 95
+ 8 8 0.450844 0.763131 96
+ 9 8 -0.779712 -1.206487 97
+ 10 8 0.325771 0.553096 98
+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/colvar.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/colvar.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..a5b7352a1bd3b436ba001821425949434114b875
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/colvar.data.reference
@@ -0,0 +1,26 @@
+#! FIELDS time phi psi ves1.bias
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET min_psi -pi
+#! SET max_psi pi
+ 0.000000 -1.238 0.894 0.000
+ 1.000000 -1.484 1.048 0.000
+ 2.000000 -1.324 0.605 0.000
+ 3.000000 -1.334 0.681 9.366
+ 4.000000 -1.461 1.392 6.831
+ 5.000000 -1.220 0.787 13.134
+ 6.000000 -1.388 1.001 14.732
+ 7.000000 -1.548 1.345 15.132
+ 8.000000 -1.843 1.329 9.341
+ 9.000000 -2.242 2.606 -0.848
+ 10.000000 -1.148 0.535 15.227
+ 11.000000 -1.758 2.075 -1.701
+ 12.000000 -1.319 3.100 -6.851
+ 13.000000 -2.991 2.899 -0.885
+ 14.000000 -1.411 0.003 3.467
+ 15.000000 -2.599 2.668 2.844
+ 16.000000 -1.461 0.262 11.905
+ 17.000000 -1.379 1.158 29.036
+ 18.000000 -1.677 0.908 25.288
+ 19.000000 -1.524 1.262 29.578
+ 20.000000 -1.200 0.953 27.706
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/config b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/config
new file mode 100644
index 0000000000000000000000000000000000000000..d9b022c5f95c12fdf3de7e32807e196863eec343
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/config
@@ -0,0 +1,3 @@
+plumed_modules=ves
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro --dump-forces forces --dump-forces-fmt=%10.6f "
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/fes.ves1.iter-10.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/fes.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..6c05757b9a77b316f3cf9af892dd3e1491331e13
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/fes.ves1.iter-10.data.reference
@@ -0,0 +1,10310 @@
+#! FIELDS phi2 psi2 ves1.fes
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+#! SET min_psi2 -pi
+#! SET max_psi2 pi
+#! SET nbins_psi2 101
+#! SET periodic_psi2 false
+ -3.141592654 -3.141592654 39.561068565
+ -3.078760801 -3.141592654 42.735764234
+ -3.015928947 -3.141592654 43.988087240
+ -2.953097094 -3.141592654 44.008818470
+ -2.890265241 -3.141592654 43.317225218
+ -2.827433388 -3.141592654 42.292186423
+ -2.764601535 -3.141592654 41.199118104
+ -2.701769682 -3.141592654 40.213115396
+ -2.638937829 -3.141592654 39.438698606
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+ -2.513274123 -3.141592654 38.687385280
+ -2.450442270 -3.141592654 38.703835435
+ -2.387610417 -3.141592654 38.939676656
+ -2.324778564 -3.141592654 39.347615532
+ -2.261946711 -3.141592654 39.875301098
+ -2.199114858 -3.141592654 40.469971642
+ -2.136283004 -3.141592654 41.081908351
+ -2.073451151 -3.141592654 41.666876490
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diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/forces.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/forces.reference
new file mode 100644
index 0000000000000000000000000000000000000000..5c813f4b6347a0ff3e6b320db25d63fc130a7a32
--- /dev/null
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diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/gradient.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/gradient.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..8cf6b53d706454b3b3b4e2a79cf5d891c345eb83
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/gradient.data.reference
@@ -0,0 +1,1100 @@
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.gradient index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
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+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/hessian.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/hessian.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..035ea73deafbb0ab8b14cacbd7ae64ac620140f0
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/hessian.data.reference
@@ -0,0 +1,1110 @@
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
+ 0 0 0.000000 0
+ 1 0 0.000316 1
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+ 10 8 0.018950 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
+ 0 0 0.000000 0
+ 1 0 0.000123 1
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+ 3 0 0.000000 3
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+ 5 0 0.001427 5
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
+ 0 0 0.000000 0
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+ 2 0 0.000556 2
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+ 10 8 0.006164 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
+ 0 0 0.000000 0
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+ 2 0 0.002891 2
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
+ 0 0 0.000000 0
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
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+ 10 8 0.103970 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
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+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
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+ 10 8 0.014248 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
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+ 6 2 0.000304 28
+ 7 2 0.012188 29
+ 8 2 0.011368 30
+ 9 2 0.000208 31
+ 10 2 0.020706 32
+ 0 3 0.000521 33
+ 1 3 0.000069 34
+ 2 3 0.003496 35
+ 3 3 0.001443 36
+ 4 3 0.003496 37
+ 5 3 0.014325 38
+ 6 3 0.001972 39
+ 7 3 0.012575 40
+ 8 3 0.030581 41
+ 9 3 0.001949 42
+ 10 3 0.027292 43
+ 0 4 0.004798 44
+ 1 4 0.003585 45
+ 2 4 0.000365 46
+ 3 4 0.006215 47
+ 4 4 0.003439 48
+ 5 4 0.000377 49
+ 6 4 0.005781 50
+ 7 4 0.003126 51
+ 8 4 0.000326 52
+ 9 4 0.005029 53
+ 10 4 0.002731 54
+ 0 5 0.000439 55
+ 1 5 0.002100 56
+ 2 5 0.002155 57
+ 3 5 0.000144 58
+ 4 5 0.009072 59
+ 5 5 0.011245 60
+ 6 5 0.000015 61
+ 7 5 0.021288 62
+ 8 5 0.026058 63
+ 9 5 0.000001 64
+ 10 5 0.038432 65
+ 0 6 0.006858 66
+ 1 6 0.002806 67
+ 2 6 0.003351 68
+ 3 6 0.010448 69
+ 4 6 0.000326 70
+ 5 6 0.009682 71
+ 6 6 0.010762 72
+ 7 6 0.000392 73
+ 8 6 0.017871 74
+ 9 6 0.009715 75
+ 10 6 0.003432 76
+ 0 7 0.008372 77
+ 1 7 0.008785 78
+ 2 7 0.000006 79
+ 3 7 0.009579 80
+ 4 7 0.014019 81
+ 5 7 0.001119 82
+ 6 7 0.008162 83
+ 7 7 0.020160 84
+ 8 7 0.004134 85
+ 9 7 0.006861 86
+ 10 7 0.026970 87
+ 0 8 0.001513 88
+ 1 8 0.000032 89
+ 2 8 0.004024 90
+ 3 8 0.003163 91
+ 4 8 0.002056 92
+ 5 8 0.015358 93
+ 6 8 0.003844 94
+ 7 8 0.009774 95
+ 8 8 0.031922 96
+ 9 8 0.003666 97
+ 10 8 0.023304 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.hessian index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+#! SET diagonal_matrix 1
+ 0 0 0.000000 0
+ 1 0 0.000802 1
+ 2 0 0.002260 2
+ 3 0 0.000013 3
+ 4 0 0.007838 4
+ 5 0 0.008014 5
+ 6 0 0.001139 6
+ 7 0 0.023739 7
+ 8 0 0.011659 8
+ 9 0 0.007584 9
+ 10 0 0.045614 10
+ 0 1 0.000729 11
+ 1 1 0.001411 12
+ 2 1 0.000259 13
+ 3 1 0.001123 14
+ 4 1 0.004624 15
+ 5 1 0.001302 16
+ 6 1 0.002483 17
+ 7 1 0.010213 18
+ 8 1 0.001943 19
+ 9 1 0.006103 20
+ 10 1 0.017141 21
+ 0 2 0.001360 22
+ 1 2 0.000065 23
+ 2 2 0.002560 24
+ 3 2 0.001616 25
+ 4 2 0.001791 26
+ 5 2 0.007640 27
+ 6 2 0.000273 28
+ 7 2 0.009458 29
+ 8 2 0.010955 30
+ 9 2 0.000691 31
+ 10 2 0.021702 32
+ 0 3 0.000537 33
+ 1 3 0.002335 34
+ 2 3 0.001667 35
+ 3 3 0.000949 36
+ 4 3 0.011809 37
+ 5 3 0.006699 38
+ 6 3 0.003836 39
+ 7 3 0.030375 40
+ 8 3 0.009840 41
+ 9 3 0.013579 42
+ 10 3 0.054630 43
+ 0 4 0.007587 44
+ 1 4 0.004556 45
+ 2 4 0.001458 46
+ 3 4 0.010239 47
+ 4 4 0.002653 48
+ 5 4 0.002841 49
+ 6 4 0.009363 50
+ 7 4 0.001149 51
+ 8 4 0.003906 52
+ 9 4 0.007553 53
+ 10 4 0.000304 54
+ 0 5 0.001614 55
+ 1 5 0.000002 56
+ 2 5 0.004564 57
+ 3 5 0.001837 58
+ 4 5 0.004798 59
+ 5 5 0.014076 60
+ 6 5 0.000084 61
+ 7 5 0.021389 62
+ 8 5 0.020243 63
+ 9 5 0.002644 64
+ 10 5 0.046811 65
+ 0 6 0.008207 66
+ 1 6 0.008099 67
+ 2 6 0.000042 68
+ 3 6 0.011617 69
+ 4 6 0.013330 70
+ 5 6 0.000051 71
+ 6 6 0.015432 72
+ 7 6 0.020436 73
+ 8 6 0.000110 74
+ 9 6 0.022880 75
+ 10 6 0.028033 76
+ 0 7 0.016401 77
+ 1 7 0.006989 78
+ 2 7 0.006790 79
+ 3 7 0.021542 80
+ 4 7 0.000719 81
+ 5 7 0.016339 82
+ 6 7 0.015283 83
+ 7 7 0.001245 84
+ 8 7 0.022964 85
+ 9 7 0.006346 86
+ 10 7 0.008528 87
+ 0 8 0.000205 88
+ 1 8 0.001636 89
+ 2 8 0.001849 90
+ 3 8 0.000416 91
+ 4 8 0.010051 92
+ 5 8 0.007063 93
+ 6 8 0.002590 94
+ 7 8 0.027326 95
+ 8 8 0.010335 96
+ 9 8 0.010936 97
+ 10 8 0.050304 98
+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/plumed.dat b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..ba7ecdda003ab7271a74ff39792396f7a3b800a7
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/plumed.dat
@@ -0,0 +1,54 @@
+# vim:ft=plumed
+
+phi: TORSION ATOMS=5,7,9,15 NOPBC
+psi: TORSION ATOMS=7,9,15,17 NOPBC
+phi2: COMBINE ARG=phi PERIODIC=NO
+psi2: COMBINE ARG=psi PERIODIC=NO
+
+bf1: BF_LEGENDRE ORDER=10 MINIMUM=-pi MAXIMUM=pi SCALED
+bf2: BF_LEGENDRE ORDER=8 MINIMUM=-pi MAXIMUM=pi SCALED
+td1: TD_WELLTEMPERED BIASFACTOR=10
+
+VES_LINEAR_EXPANSION ...
+ ARG=phi2,psi2
+ BASIS_FUNCTIONS=bf1,bf2
+ LABEL=ves1
+ TEMP=300.0
+ GRID_BINS=100,100
+ TARGET_DISTRIBUTION=td1
+... VES_LINEAR_EXPANSION
+
+# NOTE: These parameters do not reflect parameters used in real simulations!
+# This is only for testing!
+#
+
+OPT_AVERAGED_SGD ...
+ BIAS=ves1
+ STRIDE=1000
+ LABEL=o1
+ STEPSIZE=1.0
+ COEFFS_FILE=coeffs.data
+ COEFFS_OUTPUT=1
+ COEFFS_FMT=%12.6f
+ GRADIENT_FILE=gradient.data
+ GRADIENT_OUTPUT=1
+ GRADIENT_FMT=%12.6f
+ HESSIAN_FILE=hessian.data
+ HESSIAN_OUTPUT=1
+ HESSIAN_FMT=%12.6f
+ FES_OUTPUT=10
+ BIAS_OUTPUT=10
+ TARGETDIST_STRIDE=1
+ TARGETDIST_OUTPUT=10
+ TARGETDIST_AVERAGES_OUTPUT=1
+ TARGETDIST_AVERAGES_FMT=%12.6f
+... OPT_AVERAGED_SGD
+
+PRINT ...
+ STRIDE=500
+ ARG=phi,psi,ves1.bias
+ FILE=colvar.data FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist-averages.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist-averages.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..5082382f928dc6487eef2786f577a862559ec572
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist-averages.data.reference
@@ -0,0 +1,1210 @@
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 0.000000 1
+ 2 0 0.000112 2
+ 3 0 0.000000 3
+ 4 0 0.000500 4
+ 5 0 0.000000 5
+ 6 0 0.001261 6
+ 7 0 0.000000 7
+ 8 0 0.002471 8
+ 9 0 0.000000 9
+ 10 0 0.004188 10
+ 0 1 0.000000 11
+ 1 1 -0.000000 12
+ 2 1 0.000000 13
+ 3 1 -0.000000 14
+ 4 1 -0.000000 15
+ 5 1 0.000000 16
+ 6 1 -0.000000 17
+ 7 1 0.000000 18
+ 8 1 0.000000 19
+ 9 1 0.000000 20
+ 10 1 -0.000000 21
+ 0 2 0.000112 22
+ 1 2 0.000000 23
+ 2 2 0.000000 24
+ 3 2 0.000000 25
+ 4 2 0.000000 26
+ 5 2 0.000000 27
+ 6 2 0.000000 28
+ 7 2 0.000000 29
+ 8 2 0.000001 30
+ 9 2 -0.000000 31
+ 10 2 0.000001 32
+ 0 3 -0.000000 33
+ 1 3 -0.000000 34
+ 2 3 0.000000 35
+ 3 3 -0.000000 36
+ 4 3 -0.000000 37
+ 5 3 0.000000 38
+ 6 3 -0.000000 39
+ 7 3 0.000000 40
+ 8 3 -0.000000 41
+ 9 3 -0.000000 42
+ 10 3 0.000000 43
+ 0 4 0.000500 44
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+ 2 4 0.000000 46
+ 3 4 -0.000000 47
+ 4 4 0.000000 48
+ 5 4 -0.000000 49
+ 6 4 0.000001 50
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+ 8 4 0.000002 52
+ 9 4 -0.000000 53
+ 10 4 0.000004 54
+ 0 5 0.000000 55
+ 1 5 -0.000000 56
+ 2 5 0.000000 57
+ 3 5 0.000000 58
+ 4 5 -0.000000 59
+ 5 5 -0.000000 60
+ 6 5 0.000000 61
+ 7 5 -0.000000 62
+ 8 5 0.000000 63
+ 9 5 -0.000000 64
+ 10 5 0.000000 65
+ 0 6 0.001261 66
+ 1 6 0.000000 67
+ 2 6 0.000000 68
+ 3 6 0.000000 69
+ 4 6 0.000001 70
+ 5 6 -0.000000 71
+ 6 6 0.000003 72
+ 7 6 0.000000 73
+ 8 6 0.000006 74
+ 9 6 -0.000000 75
+ 10 6 0.000011 76
+ 0 7 0.000000 77
+ 1 7 -0.000000 78
+ 2 7 0.000000 79
+ 3 7 -0.000000 80
+ 4 7 0.000000 81
+ 5 7 0.000000 82
+ 6 7 0.000000 83
+ 7 7 0.000000 84
+ 8 7 -0.000000 85
+ 9 7 -0.000000 86
+ 10 7 0.000000 87
+ 0 8 0.002471 88
+ 1 8 0.000000 89
+ 2 8 0.000001 90
+ 3 8 0.000000 91
+ 4 8 0.000002 92
+ 5 8 0.000000 93
+ 6 8 0.000006 94
+ 7 8 0.000000 95
+ 8 8 0.000012 96
+ 9 8 0.000000 97
+ 10 8 0.000021 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 0.000000 1
+ 2 0 0.000112 2
+ 3 0 0.000000 3
+ 4 0 0.000500 4
+ 5 0 0.000000 5
+ 6 0 0.001261 6
+ 7 0 0.000000 7
+ 8 0 0.002471 8
+ 9 0 0.000000 9
+ 10 0 0.004188 10
+ 0 1 0.000000 11
+ 1 1 -0.000000 12
+ 2 1 0.000000 13
+ 3 1 -0.000000 14
+ 4 1 -0.000000 15
+ 5 1 0.000000 16
+ 6 1 -0.000000 17
+ 7 1 0.000000 18
+ 8 1 0.000000 19
+ 9 1 0.000000 20
+ 10 1 -0.000000 21
+ 0 2 0.000112 22
+ 1 2 0.000000 23
+ 2 2 0.000000 24
+ 3 2 0.000000 25
+ 4 2 0.000000 26
+ 5 2 0.000000 27
+ 6 2 0.000000 28
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+ 8 2 0.000001 30
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+ 0 7 0.000000 77
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+ 3 7 -0.000000 80
+ 4 7 0.000000 81
+ 5 7 0.000000 82
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+ 8 7 -0.000000 85
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+ 0 8 0.002471 88
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+ 3 8 0.000000 91
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+ 5 8 0.000000 93
+ 6 8 0.000006 94
+ 7 8 0.000000 95
+ 8 8 0.000012 96
+ 9 8 0.000000 97
+ 10 8 0.000021 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.004410 1
+ 2 0 -0.002765 2
+ 3 0 0.006888 3
+ 4 0 -0.002432 4
+ 5 0 -0.004131 5
+ 6 0 0.007615 6
+ 7 0 -0.001190 7
+ 8 0 -0.002678 8
+ 9 0 0.005683 9
+ 10 0 0.004278 10
+ 0 1 0.002851 11
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+ 2 1 -0.001337 13
+ 3 1 0.003270 14
+ 4 1 -0.001435 15
+ 5 1 -0.001908 16
+ 6 1 0.003036 17
+ 7 1 -0.000651 18
+ 8 1 -0.002336 19
+ 9 1 0.002714 20
+ 10 1 -0.000034 21
+ 0 2 -0.004917 22
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+ 5 2 0.003550 27
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+ 8 2 0.004410 30
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+ 5 3 0.003702 38
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+ 5 8 0.002659 93
+ 6 8 -0.004402 94
+ 7 8 0.001081 95
+ 8 8 0.003320 96
+ 9 8 -0.004045 97
+ 10 8 0.000309 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.007749 1
+ 2 0 -0.004650 2
+ 3 0 0.011816 3
+ 4 0 -0.004798 4
+ 5 0 -0.006810 5
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+ 7 0 -0.002542 7
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+ 6 8 -0.007257 94
+ 7 8 0.002083 95
+ 8 8 0.005163 96
+ 9 8 -0.006690 97
+ 10 8 0.000875 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.011367 1
+ 2 0 -0.006888 2
+ 3 0 0.017229 3
+ 4 0 -0.007054 4
+ 5 0 -0.010047 5
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+ 2 7 0.005160 79
+ 3 7 -0.011764 80
+ 4 7 0.004468 81
+ 5 7 0.007573 82
+ 6 7 -0.010760 83
+ 7 7 0.001193 84
+ 8 7 0.009222 85
+ 9 7 -0.009176 86
+ 10 7 -0.001583 87
+ 0 8 -0.007713 88
+ 1 8 0.007604 89
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+ 3 8 -0.011464 91
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+ 6 8 -0.010708 94
+ 7 8 0.002866 95
+ 8 8 0.007731 96
+ 9 8 -0.009679 97
+ 10 8 0.000923 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.015661 1
+ 2 0 -0.008656 2
+ 3 0 0.022933 3
+ 4 0 -0.010501 4
+ 5 0 -0.012249 5
+ 6 0 0.022260 6
+ 7 0 -0.006076 7
+ 8 0 -0.011971 8
+ 9 0 0.018181 9
+ 10 0 0.002071 10
+ 0 1 0.010997 11
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+ 4 1 -0.006228 15
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+ 7 1 -0.003848 18
+ 8 1 -0.007080 19
+ 9 1 0.009832 20
+ 10 1 -0.001792 21
+ 0 2 -0.015362 22
+ 1 2 0.011617 23
+ 2 2 0.006912 24
+ 3 2 -0.017384 25
+ 4 2 0.007849 26
+ 5 2 0.009812 27
+ 6 2 -0.015971 28
+ 7 2 0.003834 29
+ 8 2 0.011609 30
+ 9 2 -0.013749 31
+ 10 2 0.000384 32
+ 0 3 -0.019509 33
+ 1 3 0.015030 34
+ 2 3 0.008132 35
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+ 5 3 0.011234 38
+ 6 3 -0.020175 39
+ 7 3 0.006444 40
+ 8 3 0.013129 41
+ 9 3 -0.017618 42
+ 10 3 0.002649 43
+ 0 4 0.003472 44
+ 1 4 -0.001849 45
+ 2 4 -0.001967 46
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+ 4 4 -0.000424 48
+ 5 4 -0.003132 49
+ 6 4 0.003034 50
+ 7 4 0.001015 51
+ 8 4 -0.003825 52
+ 9 4 0.002281 53
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+ 0 5 0.019558 55
+ 1 5 -0.014788 56
+ 2 5 -0.008597 57
+ 3 5 0.021978 58
+ 4 5 -0.010188 59
+ 5 5 -0.012120 60
+ 6 5 0.020217 61
+ 7 5 -0.005270 62
+ 8 5 -0.014299 63
+ 9 5 0.017477 64
+ 10 5 -0.001062 65
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+ 4 6 -0.005870 70
+ 5 6 -0.003560 71
+ 6 6 0.008788 72
+ 7 6 -0.004663 73
+ 8 6 -0.003965 74
+ 9 6 0.007983 75
+ 10 6 -0.003674 76
+ 0 7 -0.012196 77
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+ 2 7 0.006113 79
+ 3 7 -0.013861 80
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+ 5 7 0.009016 82
+ 6 7 -0.012663 83
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+ 8 7 0.010890 85
+ 9 7 -0.010681 86
+ 10 7 -0.002025 87
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+ 3 8 -0.015898 91
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+ 6 8 -0.014722 94
+ 7 8 0.005145 95
+ 8 8 0.009268 96
+ 9 8 -0.013062 97
+ 10 8 0.002624 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.019844 1
+ 2 0 -0.010043 2
+ 3 0 0.028018 3
+ 4 0 -0.013676 4
+ 5 0 -0.013785 5
+ 6 0 0.026192 6
+ 7 0 -0.007972 7
+ 8 0 -0.013582 8
+ 9 0 0.020767 9
+ 10 0 0.001564 10
+ 0 1 0.014195 11
+ 1 1 -0.011396 12
+ 2 1 -0.004867 13
+ 3 1 0.015219 14
+ 4 1 -0.008620 15
+ 5 1 -0.006267 16
+ 6 1 0.013257 17
+ 7 1 -0.005358 18
+ 8 1 -0.007209 19
+ 9 1 0.010731 20
+ 10 1 -0.002064 21
+ 0 2 -0.017916 22
+ 1 2 0.013286 23
+ 2 2 0.008623 24
+ 3 2 -0.020618 25
+ 4 2 0.008815 26
+ 5 2 0.012359 27
+ 6 2 -0.019389 28
+ 7 2 0.004461 29
+ 8 2 0.014257 30
+ 9 2 -0.016845 31
+ 10 2 0.000934 32
+ 0 3 -0.023574 33
+ 1 3 0.018222 34
+ 2 3 0.009776 35
+ 3 3 -0.026416 36
+ 4 3 0.013333 37
+ 5 3 0.013414 38
+ 6 3 -0.024460 39
+ 7 3 0.008281 40
+ 8 3 0.015311 41
+ 9 3 -0.021213 42
+ 10 3 0.003955 43
+ 0 4 0.003582 44
+ 1 4 -0.001628 45
+ 2 4 -0.002560 46
+ 3 4 0.003758 47
+ 4 4 0.000144 48
+ 5 4 -0.004140 49
+ 6 4 0.003439 50
+ 7 4 0.001801 51
+ 8 4 -0.004968 52
+ 9 4 0.002637 53
+ 10 4 0.003106 54
+ 0 5 0.022853 55
+ 1 5 -0.017081 56
+ 2 5 -0.010553 57
+ 3 5 0.026072 58
+ 4 5 -0.011743 59
+ 5 5 -0.014913 60
+ 6 5 0.024422 61
+ 7 5 -0.006405 62
+ 8 5 -0.017188 63
+ 9 5 0.021248 64
+ 10 5 -0.002043 65
+ 0 6 0.010971 66
+ 1 6 -0.007880 67
+ 2 6 -0.003750 68
+ 3 6 0.011403 69
+ 4 6 -0.006822 70
+ 5 6 -0.004806 71
+ 6 6 0.011269 72
+ 7 6 -0.006132 73
+ 8 6 -0.005096 74
+ 9 6 0.010721 75
+ 10 6 -0.005893 76
+ 0 7 -0.014912 77
+ 1 7 0.011007 78
+ 2 7 0.006800 79
+ 3 7 -0.016384 80
+ 4 7 0.006582 81
+ 5 7 0.009761 82
+ 6 7 -0.014202 83
+ 7 7 0.001499 84
+ 8 7 0.011807 85
+ 9 7 -0.011133 86
+ 10 7 -0.003271 87
+ 0 8 -0.015072 88
+ 1 8 0.013838 89
+ 2 8 0.006442 90
+ 3 8 -0.019191 91
+ 4 8 0.010730 92
+ 5 8 0.008438 93
+ 6 8 -0.017364 94
+ 7 8 0.006999 95
+ 8 8 0.009820 96
+ 9 8 -0.014943 97
+ 10 8 0.003650 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.023260 1
+ 2 0 -0.011080 2
+ 3 0 0.032127 3
+ 4 0 -0.016401 4
+ 5 0 -0.014839 5
+ 6 0 0.029360 6
+ 7 0 -0.009707 7
+ 8 0 -0.014692 8
+ 9 0 0.022914 9
+ 10 0 0.000844 10
+ 0 1 0.017547 11
+ 1 1 -0.014387 12
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+ 3 1 0.018487 14
+ 4 1 -0.011163 15
+ 5 1 -0.006650 16
+ 6 1 0.015631 17
+ 7 1 -0.007037 18
+ 8 1 -0.007665 19
+ 9 1 0.012184 20
+ 10 1 -0.002676 21
+ 0 2 -0.018287 22
+ 1 2 0.013355 23
+ 2 2 0.009288 24
+ 3 2 -0.021277 25
+ 4 2 0.008698 26
+ 5 2 0.013349 27
+ 6 2 -0.020323 28
+ 7 2 0.004506 29
+ 8 2 0.015063 30
+ 9 2 -0.017768 31
+ 10 2 0.001282 32
+ 0 3 -0.025222 33
+ 1 3 0.019701 34
+ 2 3 0.010346 35
+ 3 3 -0.028087 36
+ 4 3 0.014733 37
+ 5 3 0.013968 38
+ 6 3 -0.026040 39
+ 7 3 0.009736 40
+ 8 3 0.015530 41
+ 9 3 -0.022518 42
+ 10 3 0.005438 43
+ 0 4 0.003896 44
+ 1 4 -0.001519 45
+ 2 4 -0.003397 46
+ 3 4 0.004348 47
+ 4 4 0.000788 48
+ 5 4 -0.005635 49
+ 6 4 0.004114 50
+ 7 4 0.002965 51
+ 8 4 -0.006910 52
+ 9 4 0.003355 53
+ 10 4 0.004576 54
+ 0 5 0.025082 55
+ 1 5 -0.018582 56
+ 2 5 -0.012269 57
+ 3 5 0.028809 58
+ 4 5 -0.012558 59
+ 5 5 -0.017497 60
+ 6 5 0.027288 61
+ 7 5 -0.006683 62
+ 8 5 -0.020129 63
+ 9 5 0.024023 64
+ 10 5 -0.002017 65
+ 0 6 0.012798 66
+ 1 6 -0.009191 67
+ 2 6 -0.004893 68
+ 3 6 0.013862 69
+ 4 6 -0.007925 70
+ 5 6 -0.006432 71
+ 6 6 0.013984 72
+ 7 6 -0.007319 73
+ 8 6 -0.006874 74
+ 9 6 0.013575 75
+ 10 6 -0.007375 76
+ 0 7 -0.015059 77
+ 1 7 0.011201 78
+ 2 7 0.006591 79
+ 3 7 -0.016096 80
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+ 5 7 0.009377 82
+ 6 7 -0.013389 83
+ 7 7 0.000864 84
+ 8 7 0.011340 85
+ 9 7 -0.009772 86
+ 10 7 -0.004586 87
+ 0 8 -0.015718 88
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+ 3 8 -0.019566 91
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+ 5 8 0.008091 93
+ 6 8 -0.017454 94
+ 7 8 0.007480 95
+ 8 8 0.009320 96
+ 9 8 -0.014679 97
+ 10 8 0.003773 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.026628 1
+ 2 0 -0.011250 2
+ 3 0 0.034459 3
+ 4 0 -0.017847 4
+ 5 0 -0.016306 5
+ 6 0 0.032351 6
+ 7 0 -0.011173 7
+ 8 0 -0.015998 8
+ 9 0 0.025275 9
+ 10 0 -0.000329 10
+ 0 1 0.020582 11
+ 1 1 -0.017379 12
+ 2 1 -0.004708 13
+ 3 1 0.019510 14
+ 4 1 -0.011882 15
+ 5 1 -0.007732 16
+ 6 1 0.017857 17
+ 7 1 -0.008412 18
+ 8 1 -0.008339 19
+ 9 1 0.013856 20
+ 10 1 -0.003963 21
+ 0 2 -0.018180 22
+ 1 2 0.012650 23
+ 2 2 0.010995 24
+ 3 2 -0.023174 25
+ 4 2 0.009820 26
+ 5 2 0.013293 27
+ 6 2 -0.020753 28
+ 7 2 0.004506 29
+ 8 2 0.015494 30
+ 9 2 -0.018073 31
+ 10 2 0.000681 32
+ 0 3 -0.025508 33
+ 1 3 0.019579 34
+ 2 3 0.011649 35
+ 3 3 -0.029963 36
+ 4 3 0.016464 37
+ 5 3 0.013431 38
+ 6 3 -0.026418 39
+ 7 3 0.010638 40
+ 8 3 0.015154 41
+ 9 3 -0.022622 42
+ 10 3 0.005614 43
+ 0 4 0.005237 44
+ 1 4 -0.002632 45
+ 2 4 -0.003502 46
+ 3 4 0.004698 47
+ 4 4 0.001483 48
+ 5 4 -0.007663 49
+ 6 4 0.005611 50
+ 7 4 0.003596 51
+ 8 4 -0.009131 52
+ 9 4 0.004994 53
+ 10 4 0.004948 54
+ 0 5 0.027005 55
+ 1 5 -0.020058 56
+ 2 5 -0.013237 57
+ 3 5 0.030569 58
+ 4 5 -0.012924 59
+ 5 5 -0.019643 60
+ 6 5 0.029519 61
+ 7 5 -0.006836 62
+ 8 5 -0.022533 63
+ 9 5 0.026315 64
+ 10 5 -0.002226 65
+ 0 6 0.013668 66
+ 1 6 -0.009715 67
+ 2 6 -0.005726 68
+ 3 6 0.015300 69
+ 4 6 -0.008663 70
+ 5 6 -0.007226 71
+ 6 6 0.015346 72
+ 7 6 -0.007935 73
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+ 9 6 0.015079 75
+ 10 6 -0.008164 76
+ 0 7 -0.015271 77
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+ 3 7 -0.015063 80
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+ 6 7 -0.012898 83
+ 7 7 0.000431 84
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+ 9 7 -0.009041 86
+ 10 7 -0.004949 87
+ 0 8 -0.015872 88
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+ 2 8 0.004878 90
+ 3 8 -0.017883 91
+ 4 8 0.010408 92
+ 5 8 0.008161 93
+ 6 8 -0.017124 94
+ 7 8 0.007602 95
+ 8 8 0.008724 96
+ 9 8 -0.014405 97
+ 10 8 0.004550 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.030156 1
+ 2 0 -0.011007 2
+ 3 0 0.036370 3
+ 4 0 -0.019251 4
+ 5 0 -0.017280 5
+ 6 0 0.034380 6
+ 7 0 -0.011968 7
+ 8 0 -0.017551 8
+ 9 0 0.027472 9
+ 10 0 -0.001086 10
+ 0 1 0.023537 11
+ 1 1 -0.020478 12
+ 2 1 -0.003417 13
+ 3 1 0.019909 14
+ 4 1 -0.012510 15
+ 5 1 -0.008046 16
+ 6 1 0.018761 17
+ 7 1 -0.008740 18
+ 8 1 -0.009266 19
+ 9 1 0.015183 20
+ 10 1 -0.004532 21
+ 0 2 -0.018023 22
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+ 3 2 -0.025533 25
+ 4 2 0.010922 26
+ 5 2 0.013905 27
+ 6 2 -0.022197 28
+ 7 2 0.005330 29
+ 8 2 0.015759 30
+ 9 2 -0.018774 31
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+ 0 3 -0.025396 33
+ 1 3 0.019002 34
+ 2 3 0.013114 35
+ 3 3 -0.031714 36
+ 4 3 0.017852 37
+ 5 3 0.013207 38
+ 6 3 -0.027055 39
+ 7 3 0.011669 40
+ 8 3 0.014682 41
+ 9 3 -0.022702 42
+ 10 3 0.005874 43
+ 0 4 0.006907 44
+ 1 4 -0.004025 45
+ 2 4 -0.003740 46
+ 3 4 0.005548 47
+ 4 4 0.001758 48
+ 5 4 -0.009694 49
+ 6 4 0.007525 50
+ 7 4 0.003729 51
+ 8 4 -0.011206 52
+ 9 4 0.006914 53
+ 10 4 0.004871 54
+ 0 5 0.028486 55
+ 1 5 -0.021011 56
+ 2 5 -0.014378 57
+ 3 5 0.032325 58
+ 4 5 -0.013192 59
+ 5 5 -0.021841 60
+ 6 5 0.032020 61
+ 7 5 -0.007502 62
+ 8 5 -0.024337 63
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+ 0 6 0.013396 66
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+ 4 6 -0.008736 70
+ 5 6 -0.008119 71
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+ 7 6 -0.008783 73
+ 8 6 -0.008022 74
+ 9 6 0.015783 75
+ 10 6 -0.009024 76
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+ 6 7 -0.012274 83
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+ 3 8 -0.015722 91
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+ 6 8 -0.015852 94
+ 7 8 0.006982 95
+ 8 8 0.008273 96
+ 9 8 -0.013743 97
+ 10 8 0.004730 98
+#!-------------------
+
+
+#! FIELDS idx_phi2 idx_psi2 ves1.targetdist_averages index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 2
+#! SET ncoeffs_total 99
+#! SET shape_phi2 11
+#! SET shape_psi2 9
+ 0 0 0.500000 0
+ 1 0 -0.034343 1
+ 2 0 -0.011154 2
+ 3 0 0.039442 3
+ 4 0 -0.021403 4
+ 5 0 -0.018591 5
+ 6 0 0.037423 6
+ 7 0 -0.013394 7
+ 8 0 -0.019417 8
+ 9 0 0.030554 9
+ 10 0 -0.002368 10
+ 0 1 0.026836 11
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+ 3 1 0.021032 14
+ 4 1 -0.013558 15
+ 5 1 -0.008580 16
+ 6 1 0.020211 17
+ 7 1 -0.009343 18
+ 8 1 -0.010435 19
+ 9 1 0.017012 20
+ 10 1 -0.005317 21
+ 0 2 -0.018871 22
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+ 3 2 -0.028685 25
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+ 6 2 -0.024536 28
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+ 8 2 0.016270 30
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+ 0 3 -0.026686 33
+ 1 3 0.019649 34
+ 2 3 0.014824 35
+ 3 3 -0.034761 36
+ 4 3 0.020001 37
+ 5 3 0.013611 38
+ 6 3 -0.029096 39
+ 7 3 0.013395 40
+ 8 3 0.014837 41
+ 9 3 -0.024020 42
+ 10 3 0.006728 43
+ 0 4 0.008401 44
+ 1 4 -0.005306 45
+ 2 4 -0.003912 46
+ 3 4 0.006344 47
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+ 5 4 -0.011331 49
+ 6 4 0.009178 50
+ 7 4 0.003700 51
+ 8 4 -0.012856 52
+ 9 4 0.008569 53
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+ 0 5 0.031100 55
+ 1 5 -0.022966 56
+ 2 5 -0.015737 57
+ 3 5 0.035314 58
+ 4 5 -0.014438 59
+ 5 5 -0.024134 60
+ 6 5 0.035530 61
+ 7 5 -0.008957 62
+ 8 5 -0.026239 63
+ 9 5 0.031415 64
+ 10 5 -0.004083 65
+ 0 6 0.013912 66
+ 1 6 -0.009121 67
+ 2 6 -0.007830 68
+ 3 6 0.017557 69
+ 4 6 -0.009313 70
+ 5 6 -0.009197 71
+ 6 6 0.018184 72
+ 7 6 -0.009945 73
+ 8 6 -0.008438 74
+ 9 6 0.017005 75
+ 10 6 -0.010027 76
+ 0 7 -0.017924 77
+ 1 7 0.015039 78
+ 2 7 0.003851 79
+ 3 7 -0.014603 80
+ 4 7 0.005868 81
+ 5 7 0.009169 82
+ 6 7 -0.012525 83
+ 7 7 -0.000473 84
+ 8 7 0.011952 85
+ 9 7 -0.009377 86
+ 10 7 -0.005418 87
+ 0 8 -0.017246 88
+ 1 8 0.017660 89
+ 2 8 0.001909 90
+ 3 8 -0.015257 91
+ 4 8 0.009469 92
+ 5 8 0.007620 93
+ 6 8 -0.015995 94
+ 7 8 0.007115 95
+ 8 8 0.008471 96
+ 9 8 -0.014333 97
+ 10 8 0.005427 98
+#!-------------------
+
+
diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist.ves1.iter-10.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..b3efe7d21d4d12f872aeaf5ff6acf2e55c8b7e3b
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist.ves1.iter-10.data.reference
@@ -0,0 +1,10310 @@
+#! FIELDS phi2 psi2 targetdist
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+#! SET min_psi2 -pi
+#! SET max_psi2 pi
+#! SET nbins_psi2 101
+#! SET periodic_psi2 false
+ -3.141592654 -3.141592654 0.022613639
+ -3.078760801 -3.141592654 0.019911096
+ -3.015928947 -3.141592654 0.018936108
+ -2.953097094 -3.141592654 0.018920376
+ -2.890265241 -3.141592654 0.019452312
+ -2.827433388 -3.141592654 0.020268350
+ -2.764601535 -3.141592654 0.021176298
+ -2.701769682 -3.141592654 0.022030154
+ -2.638937829 -3.141592654 0.022724852
+ -2.576105976 -3.141592654 0.023196297
+ -2.513274123 -3.141592654 0.023419755
+ -2.450442270 -3.141592654 0.023404314
+ -2.387610417 -3.141592654 0.023184068
+ -2.324778564 -3.141592654 0.022807986
+ -2.261946711 -3.141592654 0.022330543
+ -2.199114858 -3.141592654 0.021804461
+ -2.136283004 -3.141592654 0.021276040
+ -2.073451151 -3.141592654 0.020782883
+ -2.010619298 -3.141592654 0.020353417
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diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist.ves1.log.iter-10.data.reference b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist.ves1.log.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..2d3979ac63cb432b69aa8563b09dc46f977c3ecd
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/targetdist.ves1.log.iter-10.data.reference
@@ -0,0 +1,10310 @@
+#! FIELDS phi2 psi2 log_targetdist
+#! SET min_phi2 -pi
+#! SET max_phi2 pi
+#! SET nbins_phi2 101
+#! SET periodic_phi2 false
+#! SET min_psi2 -pi
+#! SET max_psi2 pi
+#! SET nbins_psi2 101
+#! SET periodic_psi2 false
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diff --git a/regtest/ves/rt-le-2d-legendre-scaled-welltempered/traj.gro b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/traj.gro
new file mode 100644
index 0000000000000000000000000000000000000000..c1c387a0144ec8021b9e5b0453be534f2ca906e2
--- /dev/null
+++ b/regtest/ves/rt-le-2d-legendre-scaled-welltempered/traj.gro
@@ -0,0 +1,525 @@
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 0.00000
+ 22
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 1.00000
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+ 3NME H 18 1.200 1.275 1.398
+ 3NME CH3 19 1.188 1.089 1.516
+ 3NME HH31 20 1.083 1.086 1.543
+ 3NME HH32 21 1.233 0.990 1.511
+ 3NME HH33 22 1.241 1.141 1.596
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 2.00000
+ 22
+ 1ACE HH31 1 1.532 1.520 1.209
+ 1ACE CH3 2 1.478 1.493 1.300
+ 1ACE HH32 3 1.465 1.586 1.356
+ 1ACE HH33 4 1.548 1.426 1.350
+ 1ACE C 5 1.352 1.423 1.279
+ 1ACE O 6 1.252 1.461 1.340
+ 2ALA N 7 1.351 1.326 1.190
+ 2ALA H 8 1.442 1.293 1.160
+ 2ALA CA 9 1.232 1.244 1.160
+ 2ALA HA 10 1.146 1.310 1.151
+ 2ALA CB 11 1.241 1.190 1.016
+ 2ALA HB1 12 1.333 1.132 1.008
+ 2ALA HB2 13 1.160 1.123 0.986
+ 2ALA HB3 14 1.242 1.280 0.955
+ 2ALA C 15 1.203 1.138 1.270
+ 2ALA O 16 1.161 1.021 1.240
+ 3NME N 17 1.230 1.171 1.396
+ 3NME H 18 1.257 1.266 1.417
+ 3NME CH3 19 1.217 1.090 1.512
+ 3NME HH31 20 1.144 1.011 1.493
+ 3NME HH32 21 1.307 1.029 1.526
+ 3NME HH33 22 1.212 1.146 1.605
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 3.00000
+ 22
+ 1ACE HH31 1 1.439 1.582 1.175
+ 1ACE CH3 2 1.474 1.516 1.254
+ 1ACE HH32 3 1.480 1.585 1.338
+ 1ACE HH33 4 1.569 1.465 1.242
+ 1ACE C 5 1.364 1.419 1.280
+ 1ACE O 6 1.277 1.446 1.367
+ 2ALA N 7 1.358 1.323 1.194
+ 2ALA H 8 1.443 1.313 1.140
+ 2ALA CA 9 1.235 1.243 1.164
+ 2ALA HA 10 1.150 1.310 1.170
+ 2ALA CB 11 1.240 1.197 1.019
+ 2ALA HB1 12 1.316 1.119 1.016
+ 2ALA HB2 13 1.145 1.157 0.982
+ 2ALA HB3 14 1.279 1.276 0.955
+ 2ALA C 15 1.201 1.137 1.272
+ 2ALA O 16 1.172 1.021 1.232
+ 3NME N 17 1.218 1.166 1.402
+ 3NME H 18 1.240 1.259 1.434
+ 3NME CH3 19 1.186 1.086 1.518
+ 3NME HH31 20 1.225 0.984 1.527
+ 3NME HH32 21 1.193 1.134 1.616
+ 3NME HH33 22 1.081 1.058 1.509
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 4.00000
+ 22
+ 1ACE HH31 1 1.549 1.508 1.196
+ 1ACE CH3 2 1.500 1.486 1.290
+ 1ACE HH32 3 1.487 1.571 1.357
+ 1ACE HH33 4 1.563 1.415 1.343
+ 1ACE C 5 1.362 1.425 1.270
+ 1ACE O 6 1.265 1.465 1.340
+ 2ALA N 7 1.349 1.324 1.182
+ 2ALA H 8 1.432 1.287 1.138
+ 2ALA CA 9 1.221 1.249 1.168
+ 2ALA HA 10 1.138 1.318 1.184
+ 2ALA CB 11 1.201 1.194 1.025
+ 2ALA HB1 12 1.276 1.117 1.005
+ 2ALA HB2 13 1.096 1.165 1.014
+ 2ALA HB3 14 1.229 1.265 0.947
+ 2ALA C 15 1.217 1.141 1.275
+ 2ALA O 16 1.234 1.024 1.243
+ 3NME N 17 1.183 1.174 1.400
+ 3NME H 18 1.184 1.274 1.412
+ 3NME CH3 19 1.187 1.078 1.509
+ 3NME HH31 20 1.248 0.990 1.490
+ 3NME HH32 21 1.220 1.120 1.604
+ 3NME HH33 22 1.088 1.035 1.527
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 5.00000
+ 22
+ 1ACE HH31 1 1.449 1.585 1.168
+ 1ACE CH3 2 1.479 1.518 1.248
+ 1ACE HH32 3 1.523 1.577 1.328
+ 1ACE HH33 4 1.565 1.461 1.213
+ 1ACE C 5 1.364 1.422 1.284
+ 1ACE O 6 1.305 1.438 1.389
+ 2ALA N 7 1.347 1.326 1.187
+ 2ALA H 8 1.423 1.328 1.122
+ 2ALA CA 9 1.226 1.241 1.162
+ 2ALA HA 10 1.139 1.308 1.162
+ 2ALA CB 11 1.236 1.193 1.023
+ 2ALA HB1 12 1.314 1.117 1.012
+ 2ALA HB2 13 1.137 1.167 0.986
+ 2ALA HB3 14 1.273 1.278 0.966
+ 2ALA C 15 1.195 1.133 1.268
+ 2ALA O 16 1.173 1.016 1.239
+ 3NME N 17 1.204 1.175 1.393
+ 3NME H 18 1.211 1.275 1.403
+ 3NME CH3 19 1.188 1.090 1.513
+ 3NME HH31 20 1.089 1.044 1.509
+ 3NME HH32 21 1.267 1.014 1.509
+ 3NME HH33 22 1.189 1.145 1.607
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 6.00000
+ 22
+ 1ACE HH31 1 1.517 1.511 1.181
+ 1ACE CH3 2 1.490 1.488 1.284
+ 1ACE HH32 3 1.482 1.582 1.339
+ 1ACE HH33 4 1.569 1.421 1.316
+ 1ACE C 5 1.359 1.414 1.282
+ 1ACE O 6 1.272 1.447 1.358
+ 2ALA N 7 1.351 1.320 1.186
+ 2ALA H 8 1.434 1.297 1.133
+ 2ALA CA 9 1.220 1.251 1.159
+ 2ALA HA 10 1.139 1.323 1.167
+ 2ALA CB 11 1.220 1.194 1.018
+ 2ALA HB1 12 1.298 1.120 1.003
+ 2ALA HB2 13 1.120 1.158 0.994
+ 2ALA HB3 14 1.224 1.286 0.960
+ 2ALA C 15 1.201 1.139 1.270
+ 2ALA O 16 1.190 1.022 1.239
+ 3NME N 17 1.203 1.178 1.393
+ 3NME H 18 1.207 1.277 1.409
+ 3NME CH3 19 1.211 1.102 1.515
+ 3NME HH31 20 1.111 1.064 1.534
+ 3NME HH32 21 1.275 1.017 1.492
+ 3NME HH33 22 1.264 1.151 1.597
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 7.00000
+ 22
+ 1ACE HH31 1 1.483 1.590 1.185
+ 1ACE CH3 2 1.505 1.501 1.245
+ 1ACE HH32 3 1.538 1.533 1.344
+ 1ACE HH33 4 1.580 1.430 1.209
+ 1ACE C 5 1.379 1.418 1.267
+ 1ACE O 6 1.298 1.443 1.349
+ 2ALA N 7 1.360 1.320 1.187
+ 2ALA H 8 1.426 1.297 1.114
+ 2ALA CA 9 1.224 1.253 1.180
+ 2ALA HA 10 1.147 1.326 1.205
+ 2ALA CB 11 1.174 1.215 1.037
+ 2ALA HB1 12 1.245 1.152 0.983
+ 2ALA HB2 13 1.084 1.154 1.032
+ 2ALA HB3 14 1.153 1.311 0.992
+ 2ALA C 15 1.212 1.141 1.280
+ 2ALA O 16 1.219 1.022 1.244
+ 3NME N 17 1.191 1.176 1.408
+ 3NME H 18 1.207 1.275 1.423
+ 3NME CH3 19 1.162 1.068 1.509
+ 3NME HH31 20 1.229 0.982 1.503
+ 3NME HH32 21 1.162 1.109 1.610
+ 3NME HH33 22 1.056 1.044 1.499
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 8.00000
+ 22
+ 1ACE HH31 1 1.576 1.425 1.169
+ 1ACE CH3 2 1.523 1.455 1.260
+ 1ACE HH32 3 1.547 1.556 1.294
+ 1ACE HH33 4 1.566 1.393 1.338
+ 1ACE C 5 1.385 1.422 1.255
+ 1ACE O 6 1.308 1.499 1.305
+ 2ALA N 7 1.346 1.311 1.189
+ 2ALA H 8 1.419 1.248 1.159
+ 2ALA CA 9 1.210 1.260 1.193
+ 2ALA HA 10 1.139 1.326 1.242
+ 2ALA CB 11 1.152 1.252 1.051
+ 2ALA HB1 12 1.230 1.210 0.987
+ 2ALA HB2 13 1.066 1.185 1.052
+ 2ALA HB3 14 1.127 1.354 1.024
+ 2ALA C 15 1.206 1.136 1.282
+ 2ALA O 16 1.195 1.023 1.229
+ 3NME N 17 1.210 1.152 1.420
+ 3NME H 18 1.221 1.243 1.463
+ 3NME CH3 19 1.185 1.048 1.518
+ 3NME HH31 20 1.195 0.948 1.475
+ 3NME HH32 21 1.261 1.070 1.593
+ 3NME HH33 22 1.088 1.064 1.565
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 9.00000
+ 22
+ 1ACE HH31 1 1.515 1.474 1.040
+ 1ACE CH3 2 1.535 1.461 1.147
+ 1ACE HH32 3 1.561 1.560 1.184
+ 1ACE HH33 4 1.612 1.386 1.165
+ 1ACE C 5 1.406 1.430 1.217
+ 1ACE O 6 1.361 1.502 1.307
+ 2ALA N 7 1.345 1.316 1.190
+ 2ALA H 8 1.384 1.254 1.121
+ 2ALA CA 9 1.217 1.277 1.242
+ 2ALA HA 10 1.187 1.348 1.319
+ 2ALA CB 11 1.111 1.278 1.134
+ 2ALA HB1 12 1.129 1.198 1.062
+ 2ALA HB2 13 1.018 1.269 1.189
+ 2ALA HB3 14 1.121 1.372 1.079
+ 2ALA C 15 1.217 1.133 1.309
+ 2ALA O 16 1.293 1.044 1.265
+ 3NME N 17 1.132 1.116 1.408
+ 3NME H 18 1.076 1.195 1.437
+ 3NME CH3 19 1.112 1.003 1.490
+ 3NME HH31 20 1.156 0.910 1.456
+ 3NME HH32 21 1.153 1.026 1.588
+ 3NME HH33 22 1.005 0.985 1.500
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 10.00000
+ 22
+ 1ACE HH31 1 1.536 1.485 1.135
+ 1ACE CH3 2 1.521 1.460 1.240
+ 1ACE HH32 3 1.528 1.557 1.289
+ 1ACE HH33 4 1.602 1.397 1.276
+ 1ACE C 5 1.385 1.401 1.261
+ 1ACE O 6 1.341 1.416 1.373
+ 2ALA N 7 1.322 1.332 1.167
+ 2ALA H 8 1.364 1.316 1.076
+ 2ALA CA 9 1.190 1.273 1.177
+ 2ALA HA 10 1.125 1.352 1.216
+ 2ALA CB 11 1.134 1.230 1.038
+ 2ALA HB1 12 1.167 1.128 1.016
+ 2ALA HB2 13 1.026 1.238 1.046
+ 2ALA HB3 14 1.174 1.287 0.953
+ 2ALA C 15 1.183 1.157 1.283
+ 2ALA O 16 1.111 1.061 1.259
+ 3NME N 17 1.264 1.157 1.396
+ 3NME H 18 1.320 1.241 1.405
+ 3NME CH3 19 1.264 1.070 1.510
+ 3NME HH31 20 1.163 1.057 1.548
+ 3NME HH32 21 1.311 0.974 1.487
+ 3NME HH33 22 1.326 1.109 1.592
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 11.00000
+ 22
+ 1ACE HH31 1 1.607 1.359 1.178
+ 1ACE CH3 2 1.535 1.442 1.176
+ 1ACE HH32 3 1.521 1.470 1.072
+ 1ACE HH33 4 1.569 1.533 1.224
+ 1ACE C 5 1.402 1.412 1.242
+ 1ACE O 6 1.368 1.454 1.350
+ 2ALA N 7 1.319 1.332 1.177
+ 2ALA H 8 1.363 1.279 1.103
+ 2ALA CA 9 1.194 1.289 1.231
+ 2ALA HA 10 1.153 1.355 1.308
+ 2ALA CB 11 1.092 1.300 1.113
+ 2ALA HB1 12 1.137 1.243 1.032
+ 2ALA HB2 13 1.001 1.243 1.131
+ 2ALA HB3 14 1.070 1.405 1.095
+ 2ALA C 15 1.198 1.143 1.290
+ 2ALA O 16 1.237 1.057 1.213
+ 3NME N 17 1.171 1.126 1.422
+ 3NME H 18 1.164 1.213 1.472
+ 3NME CH3 19 1.200 1.009 1.496
+ 3NME HH31 20 1.118 0.938 1.493
+ 3NME HH32 21 1.284 0.953 1.454
+ 3NME HH33 22 1.230 1.031 1.598
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 12.00000
+ 22
+ 1ACE HH31 1 1.491 1.569 1.138
+ 1ACE CH3 2 1.511 1.462 1.134
+ 1ACE HH32 3 1.614 1.449 1.166
+ 1ACE HH33 4 1.495 1.444 1.028
+ 1ACE C 5 1.416 1.394 1.229
+ 1ACE O 6 1.445 1.392 1.345
+ 2ALA N 7 1.299 1.357 1.181
+ 2ALA H 8 1.278 1.358 1.082
+ 2ALA CA 9 1.196 1.301 1.267
+ 2ALA HA 10 1.185 1.364 1.355
+ 2ALA CB 11 1.063 1.319 1.182
+ 2ALA HB1 12 1.057 1.248 1.100
+ 2ALA HB2 13 0.976 1.288 1.240
+ 2ALA HB3 14 1.037 1.423 1.161
+ 2ALA C 15 1.226 1.161 1.304
+ 2ALA O 16 1.317 1.094 1.258
+ 3NME N 17 1.135 1.110 1.387
+ 3NME H 18 1.064 1.174 1.419
+ 3NME CH3 19 1.121 0.972 1.429
+ 3NME HH31 20 1.163 0.900 1.358
+ 3NME HH32 21 1.177 0.954 1.520
+ 3NME HH33 22 1.016 0.942 1.428
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 13.00000
+ 22
+ 1ACE HH31 1 1.528 1.537 1.077
+ 1ACE CH3 2 1.543 1.448 1.137
+ 1ACE HH32 3 1.634 1.463 1.195
+ 1ACE HH33 4 1.560 1.362 1.072
+ 1ACE C 5 1.421 1.428 1.229
+ 1ACE O 6 1.396 1.520 1.301
+ 2ALA N 7 1.355 1.314 1.219
+ 2ALA H 8 1.385 1.241 1.156
+ 2ALA CA 9 1.249 1.276 1.311
+ 2ALA HA 10 1.297 1.288 1.409
+ 2ALA CB 11 1.122 1.359 1.284
+ 2ALA HB1 12 1.072 1.325 1.193
+ 2ALA HB2 13 1.053 1.352 1.367
+ 2ALA HB3 14 1.153 1.463 1.275
+ 2ALA C 15 1.204 1.131 1.290
+ 2ALA O 16 1.225 1.070 1.185
+ 3NME N 17 1.131 1.077 1.382
+ 3NME H 18 1.104 1.132 1.463
+ 3NME CH3 19 1.083 0.939 1.380
+ 3NME HH31 20 1.012 0.925 1.298
+ 3NME HH32 21 1.168 0.871 1.372
+ 3NME HH33 22 1.036 0.915 1.475
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 14.00000
+ 22
+ 1ACE HH31 1 1.543 1.468 1.123
+ 1ACE CH3 2 1.548 1.443 1.229
+ 1ACE HH32 3 1.566 1.540 1.276
+ 1ACE HH33 4 1.634 1.382 1.257
+ 1ACE C 5 1.420 1.385 1.285
+ 1ACE O 6 1.412 1.375 1.404
+ 2ALA N 7 1.324 1.361 1.200
+ 2ALA H 8 1.345 1.354 1.101
+ 2ALA CA 9 1.189 1.323 1.244
+ 2ALA HA 10 1.163 1.394 1.323
+ 2ALA CB 11 1.094 1.344 1.125
+ 2ALA HB1 12 1.098 1.270 1.045
+ 2ALA HB2 13 0.995 1.352 1.170
+ 2ALA HB3 14 1.120 1.440 1.079
+ 2ALA C 15 1.166 1.169 1.284
+ 2ALA O 16 1.055 1.145 1.330
+ 3NME N 17 1.263 1.077 1.279
+ 3NME H 18 1.356 1.102 1.247
+ 3NME CH3 19 1.246 0.942 1.335
+ 3NME HH31 20 1.142 0.911 1.345
+ 3NME HH32 21 1.293 0.868 1.270
+ 3NME HH33 22 1.292 0.934 1.434
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 15.00000
+ 22
+ 1ACE HH31 1 1.508 1.417 1.043
+ 1ACE CH3 2 1.539 1.448 1.143
+ 1ACE HH32 3 1.565 1.553 1.146
+ 1ACE HH33 4 1.630 1.395 1.169
+ 1ACE C 5 1.438 1.410 1.253
+ 1ACE O 6 1.429 1.471 1.356
+ 2ALA N 7 1.348 1.327 1.217
+ 2ALA H 8 1.362 1.285 1.126
+ 2ALA CA 9 1.233 1.289 1.298
+ 2ALA HA 10 1.269 1.295 1.401
+ 2ALA CB 11 1.107 1.379 1.286
+ 2ALA HB1 12 1.057 1.360 1.191
+ 2ALA HB2 13 1.034 1.369 1.366
+ 2ALA HB3 14 1.141 1.482 1.282
+ 2ALA C 15 1.192 1.141 1.266
+ 2ALA O 16 1.220 1.089 1.156
+ 3NME N 17 1.131 1.075 1.364
+ 3NME H 18 1.117 1.126 1.450
+ 3NME CH3 19 1.090 0.931 1.376
+ 3NME HH31 20 1.156 0.880 1.446
+ 3NME HH32 21 0.996 0.929 1.431
+ 3NME HH33 22 1.090 0.874 1.283
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 16.00000
+ 22
+ 1ACE HH31 1 1.587 1.386 1.166
+ 1ACE CH3 2 1.554 1.425 1.262
+ 1ACE HH32 3 1.559 1.534 1.266
+ 1ACE HH33 4 1.627 1.390 1.335
+ 1ACE C 5 1.417 1.372 1.300
+ 1ACE O 6 1.390 1.364 1.421
+ 2ALA N 7 1.334 1.344 1.205
+ 2ALA H 8 1.365 1.367 1.111
+ 2ALA CA 9 1.190 1.324 1.235
+ 2ALA HA 10 1.160 1.386 1.319
+ 2ALA CB 11 1.105 1.363 1.112
+ 2ALA HB1 12 1.129 1.297 1.029
+ 2ALA HB2 13 0.999 1.351 1.131
+ 2ALA HB3 14 1.125 1.467 1.088
+ 2ALA C 15 1.162 1.180 1.282
+ 2ALA O 16 1.054 1.128 1.258
+ 3NME N 17 1.261 1.106 1.318
+ 3NME H 18 1.349 1.152 1.336
+ 3NME CH3 19 1.250 0.960 1.324
+ 3NME HH31 20 1.264 0.908 1.229
+ 3NME HH32 21 1.322 0.926 1.399
+ 3NME HH33 22 1.153 0.923 1.357
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 17.00000
+ 22
+ 1ACE HH31 1 1.614 1.382 1.173
+ 1ACE CH3 2 1.559 1.432 1.253
+ 1ACE HH32 3 1.547 1.532 1.213
+ 1ACE HH33 4 1.625 1.444 1.339
+ 1ACE C 5 1.426 1.380 1.288
+ 1ACE O 6 1.411 1.348 1.406
+ 2ALA N 7 1.325 1.370 1.200
+ 2ALA H 8 1.341 1.388 1.102
+ 2ALA CA 9 1.189 1.318 1.239
+ 2ALA HA 10 1.170 1.358 1.338
+ 2ALA CB 11 1.084 1.388 1.158
+ 2ALA HB1 12 1.113 1.369 1.055
+ 2ALA HB2 13 0.994 1.336 1.189
+ 2ALA HB3 14 1.075 1.493 1.186
+ 2ALA C 15 1.170 1.163 1.252
+ 2ALA O 16 1.097 1.103 1.171
+ 3NME N 17 1.235 1.099 1.349
+ 3NME H 18 1.305 1.153 1.399
+ 3NME CH3 19 1.220 0.964 1.393
+ 3NME HH31 20 1.315 0.912 1.406
+ 3NME HH32 21 1.168 0.953 1.489
+ 3NME HH33 22 1.178 0.897 1.318
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 18.00000
+ 22
+ 1ACE HH31 1 1.555 1.419 1.126
+ 1ACE CH3 2 1.554 1.431 1.235
+ 1ACE HH32 3 1.554 1.535 1.267
+ 1ACE HH33 4 1.638 1.381 1.283
+ 1ACE C 5 1.423 1.378 1.292
+ 1ACE O 6 1.416 1.347 1.409
+ 2ALA N 7 1.322 1.351 1.211
+ 2ALA H 8 1.350 1.370 1.115
+ 2ALA CA 9 1.185 1.318 1.251
+ 2ALA HA 10 1.171 1.358 1.352
+ 2ALA CB 11 1.091 1.400 1.149
+ 2ALA HB1 12 1.059 1.346 1.060
+ 2ALA HB2 13 1.008 1.443 1.205
+ 2ALA HB3 14 1.154 1.480 1.109
+ 2ALA C 15 1.163 1.166 1.255
+ 2ALA O 16 1.060 1.108 1.214
+ 3NME N 17 1.255 1.102 1.328
+ 3NME H 18 1.335 1.159 1.354
+ 3NME CH3 19 1.246 0.964 1.369
+ 3NME HH31 20 1.154 0.913 1.344
+ 3NME HH32 21 1.323 0.899 1.327
+ 3NME HH33 22 1.251 0.953 1.477
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 19.00000
+ 22
+ 1ACE HH31 1 1.559 1.326 1.133
+ 1ACE CH3 2 1.552 1.413 1.200
+ 1ACE HH32 3 1.538 1.504 1.142
+ 1ACE HH33 4 1.631 1.428 1.273
+ 1ACE C 5 1.426 1.375 1.280
+ 1ACE O 6 1.428 1.345 1.398
+ 2ALA N 7 1.319 1.363 1.209
+ 2ALA H 8 1.322 1.382 1.110
+ 2ALA CA 9 1.191 1.329 1.265
+ 2ALA HA 10 1.186 1.364 1.368
+ 2ALA CB 11 1.075 1.391 1.178
+ 2ALA HB1 12 1.098 1.383 1.072
+ 2ALA HB2 13 0.980 1.348 1.211
+ 2ALA HB3 14 1.066 1.499 1.192
+ 2ALA C 15 1.169 1.174 1.275
+ 2ALA O 16 1.086 1.118 1.203
+ 3NME N 17 1.233 1.105 1.363
+ 3NME H 18 1.312 1.150 1.405
+ 3NME CH3 19 1.242 0.956 1.350
+ 3NME HH31 20 1.219 0.899 1.440
+ 3NME HH32 21 1.165 0.918 1.284
+ 3NME HH33 22 1.333 0.921 1.301
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 20.00000
+ 22
+ 1ACE HH31 1 1.622 1.459 1.287
+ 1ACE CH3 2 1.546 1.434 1.214
+ 1ACE HH32 3 1.578 1.365 1.135
+ 1ACE HH33 4 1.509 1.531 1.180
+ 1ACE C 5 1.430 1.358 1.283
+ 1ACE O 6 1.444 1.310 1.394
+ 2ALA N 7 1.315 1.370 1.215
+ 2ALA H 8 1.323 1.427 1.132
+ 2ALA CA 9 1.178 1.334 1.258
+ 2ALA HA 10 1.163 1.376 1.357
+ 2ALA CB 11 1.079 1.393 1.158
+ 2ALA HB1 12 1.096 1.348 1.060
+ 2ALA HB2 13 0.979 1.367 1.192
+ 2ALA HB3 14 1.087 1.501 1.165
+ 2ALA C 15 1.163 1.177 1.270
+ 2ALA O 16 1.073 1.114 1.216
+ 3NME N 17 1.249 1.110 1.347
+ 3NME H 18 1.324 1.165 1.388
+ 3NME CH3 19 1.242 0.964 1.360
+ 3NME HH31 20 1.325 0.920 1.416
+ 3NME HH32 21 1.151 0.938 1.414
+ 3NME HH33 22 1.221 0.913 1.266
+ 10.00000 10.00000 10.00000
diff --git a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/colvar.data.reference b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/colvar.data.reference
index 24869d91636ba87e3d954f0c6db840485c041ab8..0868bd70a74816e46e9734d1187832eaab412d32 100644
--- a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/colvar.data.reference
+++ b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/colvar.data.reference
@@ -1,24 +1,24 @@
-#! FIELDS time phi ves1.bias o1.gradrms o1.gradmax
+#! FIELDS time phi ves1.bias
#! SET min_phi -pi
#! SET max_phi pi
- 0.000000 -1.238 0.000 0.000 0.000
- 1.000000 -1.484 0.000 0.000 0.000
- 2.000000 -1.324 0.000 0.637 0.970
- 3.000000 -1.334 4.716 0.637 0.970
- 4.000000 -1.461 4.403 0.659 0.983
- 5.000000 -1.220 6.371 0.659 0.983
- 6.000000 -1.388 7.123 0.649 0.961
- 7.000000 -1.548 7.766 0.649 0.961
- 8.000000 -1.843 1.066 0.599 0.981
- 9.000000 -2.242 -3.365 0.599 0.981
- 10.000000 -1.148 8.387 0.439 0.847
- 11.000000 -1.758 5.325 0.439 0.847
- 12.000000 -1.319 12.218 0.523 0.975
- 13.000000 -2.991 -1.208 0.523 0.975
- 14.000000 -1.411 14.007 0.475 0.814
- 15.000000 -2.599 -0.724 0.475 0.814
- 16.000000 -1.461 15.304 0.451 0.755
- 17.000000 -1.379 17.133 0.451 0.755
- 18.000000 -1.677 11.559 0.598 0.988
- 19.000000 -1.524 17.994 0.598 0.988
- 20.000000 -1.200 15.348 0.585 0.965
+ 0.000000 -1.238 0.000
+ 1.000000 -1.484 0.000
+ 2.000000 -1.324 0.000
+ 3.000000 -1.334 4.716
+ 4.000000 -1.461 4.403
+ 5.000000 -1.220 6.371
+ 6.000000 -1.388 7.123
+ 7.000000 -1.548 7.766
+ 8.000000 -1.843 1.066
+ 9.000000 -2.242 -3.365
+ 10.000000 -1.148 8.387
+ 11.000000 -1.758 5.325
+ 12.000000 -1.319 12.218
+ 13.000000 -2.991 -1.208
+ 14.000000 -1.411 14.007
+ 15.000000 -2.599 -0.724
+ 16.000000 -1.461 15.304
+ 17.000000 -1.379 17.133
+ 18.000000 -1.677 11.559
+ 19.000000 -1.524 17.994
+ 20.000000 -1.200 15.348
diff --git a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/plumed.dat b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/plumed.dat
index 83edb9d941b08f710ad4be36dda41772530b40f4..8c91d9c00a5f93e0e219a5a0793771dae4926f1d 100644
--- a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/plumed.dat
+++ b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver-2/plumed.dat
@@ -35,7 +35,7 @@ OPT_AVERAGED_SGD ...
PRINT ...
STRIDE=500
- ARG=phi,ves1.bias,o1.*
+ ARG=phi,ves1.bias
FILE=colvar.data FMT=%6.3f
... PRINT
diff --git a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/colvar.data.reference b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/colvar.data.reference
index 0c1a8c5a0caae6b9ccb5a7d835816229b1ea175c..d138bff4a5d7dd914a4f5b4f905513a5ff160750 100644
--- a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/colvar.data.reference
+++ b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/colvar.data.reference
@@ -1,24 +1,24 @@
-#! FIELDS time phi ves1.bias o1.gradrms o1.gradmax
+#! FIELDS time phi ves1.bias
#! SET min_phi -pi
#! SET max_phi pi
- 0.000000 -1.238 0.000 0.000 0.000
- 1.000000 -1.484 0.000 0.000 0.000
- 2.000000 -1.324 0.000 0.637 0.970
- 3.000000 -1.334 4.716 0.637 0.970
- 4.000000 -1.461 4.403 0.659 0.983
- 5.000000 -1.220 8.417 0.659 0.983
- 6.000000 -1.388 9.566 0.649 0.961
- 7.000000 -1.548 11.484 0.649 0.961
- 8.000000 -1.843 1.350 0.599 0.981
- 9.000000 -2.242 -4.484 0.599 0.981
- 10.000000 -1.148 11.426 0.439 0.847
- 11.000000 -1.758 8.505 0.439 0.847
- 12.000000 -1.319 17.398 0.523 0.975
- 13.000000 -2.991 -2.357 0.523 0.975
- 14.000000 -1.411 21.113 0.475 0.814
- 15.000000 -2.599 -0.596 0.475 0.814
- 16.000000 -1.461 23.344 0.451 0.755
- 17.000000 -1.379 25.813 0.451 0.755
- 18.000000 -1.677 17.779 0.598 0.988
- 19.000000 -1.524 28.684 0.598 0.988
- 20.000000 -1.200 22.933 0.585 0.965
+ 0.000000 -1.238 0.000
+ 1.000000 -1.484 0.000
+ 2.000000 -1.324 0.000
+ 3.000000 -1.334 4.716
+ 4.000000 -1.461 4.403
+ 5.000000 -1.220 8.417
+ 6.000000 -1.388 9.566
+ 7.000000 -1.548 11.484
+ 8.000000 -1.843 1.350
+ 9.000000 -2.242 -4.484
+ 10.000000 -1.148 11.426
+ 11.000000 -1.758 8.505
+ 12.000000 -1.319 17.398
+ 13.000000 -2.991 -2.357
+ 14.000000 -1.411 21.113
+ 15.000000 -2.599 -0.596
+ 16.000000 -1.461 23.344
+ 17.000000 -1.379 25.813
+ 18.000000 -1.677 17.779
+ 19.000000 -1.524 28.684
+ 20.000000 -1.200 22.933
diff --git a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/plumed.dat b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/plumed.dat
index 6feca1ee99a05d0e445fc737abedeca22fe92ac0..0c309e09f2f9b11a64d8737f614d94a66d9b7c4f 100644
--- a/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/plumed.dat
+++ b/regtest/ves/rt-opt-averaged-sgd-exp-decaying-aver/plumed.dat
@@ -35,7 +35,7 @@ OPT_AVERAGED_SGD ...
PRINT ...
STRIDE=500
- ARG=phi,ves1.bias,o1.*
+ ARG=phi,ves1.bias
FILE=colvar.data FMT=%6.3f
... PRINT
diff --git a/regtest/ves/rt-opt-averaged-sgd-maskfile/colvar.data.reference b/regtest/ves/rt-opt-averaged-sgd-maskfile/colvar.data.reference
index 7ccf565f61c8f645c5f4051f9685a51a6f63ce85..05a9c05c7776a6612c1a2645cf531e3a15de4e0b 100644
--- a/regtest/ves/rt-opt-averaged-sgd-maskfile/colvar.data.reference
+++ b/regtest/ves/rt-opt-averaged-sgd-maskfile/colvar.data.reference
@@ -1,24 +1,24 @@
-#! FIELDS time phi ves1.bias o1.gradrms o1.gradmax
+#! FIELDS time phi ves1.bias
#! SET min_phi -pi
#! SET max_phi pi
- 0.000000 -1.238 0.000 0.000 0.000
- 1.000000 -1.484 0.000 0.000 0.000
- 2.000000 -1.324 0.000 0.637 0.970
- 3.000000 -1.334 3.269 0.637 0.970
- 4.000000 -1.461 3.220 0.659 0.983
- 5.000000 -1.220 4.325 0.659 0.983
- 6.000000 -1.388 5.057 0.649 0.961
- 7.000000 -1.548 6.027 0.649 0.961
- 8.000000 -1.843 1.879 0.599 0.981
- 9.000000 -2.242 -1.819 0.599 0.981
- 10.000000 -1.148 5.786 0.439 0.847
- 11.000000 -1.758 5.171 0.439 0.847
- 12.000000 -1.319 8.648 0.523 0.975
- 13.000000 -2.991 1.784 0.523 0.975
- 14.000000 -1.411 10.083 0.475 0.814
- 15.000000 -2.599 1.350 0.475 0.814
- 16.000000 -1.461 11.032 0.451 0.755
- 17.000000 -1.379 11.862 0.451 0.755
- 18.000000 -1.677 9.170 0.598 0.988
- 19.000000 -1.524 12.659 0.598 0.988
- 20.000000 -1.200 10.287 0.585 0.965
+ 0.000000 -1.238 0.000
+ 1.000000 -1.484 0.000
+ 2.000000 -1.324 0.000
+ 3.000000 -1.334 3.269
+ 4.000000 -1.461 3.220
+ 5.000000 -1.220 4.325
+ 6.000000 -1.388 5.057
+ 7.000000 -1.548 6.027
+ 8.000000 -1.843 1.879
+ 9.000000 -2.242 -1.819
+ 10.000000 -1.148 5.786
+ 11.000000 -1.758 5.171
+ 12.000000 -1.319 8.648
+ 13.000000 -2.991 1.784
+ 14.000000 -1.411 10.083
+ 15.000000 -2.599 1.350
+ 16.000000 -1.461 11.032
+ 17.000000 -1.379 11.862
+ 18.000000 -1.677 9.170
+ 19.000000 -1.524 12.659
+ 20.000000 -1.200 10.287
diff --git a/regtest/ves/rt-opt-averaged-sgd-maskfile/plumed.dat b/regtest/ves/rt-opt-averaged-sgd-maskfile/plumed.dat
index 94944311103fb0f4c42e992ec300cf3587a21c99..a8b1210974008274163c3a2de475a15b0126e912 100644
--- a/regtest/ves/rt-opt-averaged-sgd-maskfile/plumed.dat
+++ b/regtest/ves/rt-opt-averaged-sgd-maskfile/plumed.dat
@@ -33,7 +33,7 @@ OPT_AVERAGED_SGD ...
PRINT ...
STRIDE=500
- ARG=phi,ves1.bias,o1.*
+ ARG=phi,ves1.bias
FILE=colvar.data FMT=%6.3f
... PRINT
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/Makefile b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/bias.ves1.iter-10.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/bias.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..55fc4b90e0bb8e0a74059ba4d1ad0bc14e44ef67
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/bias.ves1.iter-10.data.reference
@@ -0,0 +1,105 @@
+#! FIELDS phi ves1.bias der_phi
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET nbins_phi 100
+#! SET periodic_phi true
+ -3.141592654 -1.962887340 -12.338802116
+ -3.078760801 -1.169414064 -12.715200498
+ -3.015928947 -0.391297555 -11.842670932
+ -2.953097094 0.293014687 -9.744489584
+ -2.890265241 0.810780738 -6.578621340
+ -2.827433388 1.103213002 -2.628636251
+ -2.764601535 1.132736781 1.718540218
+ -2.701769682 0.888479952 6.006285748
+ -2.638937829 0.389363553 9.750412598
+ -2.576105976 -0.315622008 12.485919949
+ -2.513274123 -1.150108758 13.813956198
+ -2.450442270 -2.015880754 13.444439030
+ -2.387610417 -2.800832289 11.230078693
+ -2.324778564 -3.388698586 7.188264732
+ -2.261946711 -3.669712459 1.508346390
+ -2.199114858 -3.551225879 -5.456835497
+ -2.136283004 -2.967309202 -13.214845369
+ -2.073451151 -1.886407100 -21.171200499
+ -2.010619298 -0.316284409 -28.677475468
+ -1.947787445 1.694275951 -35.085823711
+ -1.884955592 4.057277381 -39.805102330
+ -1.822123739 6.650758491 -42.353552663
+ -1.759291886 9.327116398 -42.403222481
+ -1.696460033 11.923851076 -39.811998967
+ -1.633628180 14.275849793 -34.640194909
+ -1.570796327 16.228180200 -27.149996573
+ -1.507964474 17.648302059 -17.787615275
+ -1.445132621 18.436646858 -7.149543685
+ -1.382300768 18.534648860 4.064242212
+ -1.319468915 17.929528507 15.106108250
+ -1.256637061 16.655410154 25.240764953
+ -1.193805208 14.790675170 33.804217774
+ -1.130973355 12.451779631 40.256530152
+ -1.068141502 9.784073053 44.223828351
+ -1.005309649 6.950413066 45.525955652
+ -0.942477796 4.118557135 44.187485578
+ -0.879645943 1.448409775 40.431307959
+ -0.816814090 -0.919796122 34.655567695
+ -0.753982237 -2.875401651 27.396218871
+ -0.691150384 -4.344509048 19.278719545
+ -0.628318531 -5.293907399 10.963319829
+ -0.565486678 -5.731488729 3.088904596
+ -0.502654825 -5.703221985 -3.779600964
+ -0.439822972 -5.287056426 -9.195669122
+ -0.376991118 -4.584390419 -12.863688798
+ -0.314159265 -3.709942861 -14.656970625
+ -0.251327412 -2.780984749 -14.620029905
+ -0.188495559 -1.906918090 -12.955414618
+ -0.125663706 -1.180127187 -9.996768596
+ -0.062831853 -0.668881003 -6.171056989
+ 0.000000000 -0.412850137 -1.953818247
+ 0.062831853 -0.421539575 2.178140178
+ 0.125663706 -0.675654705 5.792062628
+ 0.188495559 -1.131140428 8.538354992
+ 0.251327412 -1.725387947 10.179965544
+ 0.314159265 -2.384913757 10.609550868
+ 0.376991118 -3.033697597 9.853189732
+ 0.439822972 -3.601330342 8.060748792
+ 0.502654825 -4.030170819 5.484305244
+ 0.565486678 -4.280835606 2.447166697
+ 0.628318531 -4.335534258 -0.693110509
+ 0.691150384 -4.198993981 -3.583796504
+ 0.753982237 -3.896968936 -5.914139727
+ 0.816814090 -3.472574521 -7.446871847
+ 0.879645943 -2.980902025 -8.041001900
+ 0.942477796 -2.482532833 -7.663790383
+ 1.005309649 -2.036668522 -6.390943538
+ 1.068141502 -1.694615038 -4.395294320
+ 1.130973355 -1.494304801 -1.925415089
+ 1.193805208 -1.456416832 0.723380390
+ 1.256637061 -1.582475512 3.242441860
+ 1.319468915 -1.855092601 5.343983442
+ 1.382300768 -2.240287277 6.792439000
+ 1.445132621 -2.691599109 7.429676026
+ 1.507964474 -3.155521657 7.191454953
+ 1.570796327 -3.577648783 6.113468227
+ 1.633628180 -3.908855525 4.326406440
+ 1.696460033 -4.110837235 2.040661900
+ 1.759291886 -4.160404057 -0.477626840
+ 1.822123739 -4.052064683 -2.936575167
+ 1.884955592 -3.798619184 -5.051347997
+ 1.947787445 -3.429696029 -6.576207401
+ 2.010619298 -2.988390547 -7.332346000
+ 2.073451151 -2.526367898 -7.228480223
+ 2.136283004 -2.097961365 -6.271936183
+ 2.199114858 -1.753908884 -4.568960171
+ 2.261946711 -1.535415076 -2.314123056
+ 2.324778564 -1.469197662 0.230153754
+ 2.387610417 -1.564078476 2.761863469
+ 2.450442270 -1.809520038 4.972532009
+ 2.513274123 -2.176304947 6.581698361
+ 2.576105976 -2.619327928 7.369072046
+ 2.638937829 -3.082242736 7.200869631
+ 2.701769682 -3.503501849 6.047385643
+ 2.764601535 -3.823167726 3.989720592
+ 2.827433388 -3.989777340 1.214684827
+ 2.890265241 -3.966517945 -2.001887206
+ 2.953097094 -3.736025222 -5.321964767
+ 3.015928947 -3.303241013 -8.379756402
+ 3.078760801 -2.695955240 -10.820370974
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/coeffs.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/coeffs.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..478cffec045c1a8bfd01d84cb123d22f99f8168b
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/coeffs.data.reference
@@ -0,0 +1,231 @@
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.000000 0.000000 1
+ 2 0.000000 0.000000 2
+ 3 0.000000 0.000000 3
+ 4 0.000000 0.000000 4
+ 5 0.000000 0.000000 5
+ 6 0.000000 0.000000 6
+ 7 0.000000 0.000000 7
+ 8 0.000000 0.000000 8
+ 9 0.000000 0.000000 9
+ 10 0.000000 0.000000 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.219197 0.219197 1
+ 2 -0.970366 -0.970366 2
+ 3 -0.884094 -0.884094 3
+ 4 -0.421298 -0.421298 4
+ 5 -0.590820 -0.590820 5
+ 6 0.748809 0.748809 6
+ 7 0.576392 0.576392 7
+ 8 0.715341 0.715341 8
+ 9 0.786645 0.786645 9
+ 10 -0.381816 -0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.305152 0.391107 1
+ 2 -1.461895 -1.953423 2
+ 3 -1.350614 -1.817134 3
+ 4 -0.589608 -0.757918 4
+ 5 -0.834473 -1.078125 5
+ 6 1.174985 1.601160 6
+ 7 0.948813 1.321234 7
+ 8 1.024273 1.333206 8
+ 9 1.148264 1.509884 9
+ 10 -0.689625 -0.997434 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.421218 0.653351 1
+ 2 -1.946133 -2.914610 2
+ 3 -1.788707 -2.664892 3
+ 4 -0.812257 -1.257555 4
+ 5 -1.146186 -1.769612 5
+ 6 1.540202 2.270638 6
+ 7 1.220946 1.765213 7
+ 8 1.401662 2.156440 8
+ 9 1.564119 2.395830 9
+ 10 -0.857540 -1.193370 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.448007 0.528372 1
+ 2 -2.433590 -3.895961 2
+ 3 -2.239120 -3.590362 3
+ 4 -0.861012 -1.007276 4
+ 5 -1.209573 -1.399733 5
+ 6 1.931358 3.104824 6
+ 7 1.535645 2.479741 7
+ 8 1.472935 1.686754 8
+ 9 1.639154 1.864258 9
+ 10 -1.086629 -1.773897 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.441146 0.413704 1
+ 2 -2.895058 -4.740930 2
+ 3 -2.593087 -4.008954 3
+ 4 -0.858951 -0.850710 4
+ 5 -1.239599 -1.359702 5
+ 6 2.140456 2.976852 6
+ 7 1.611231 1.913575 7
+ 8 1.562246 1.919487 8
+ 9 1.789475 2.390761 9
+ 10 -1.071904 -1.013004 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.441948 0.445955 1
+ 2 -3.365271 -5.716337 2
+ 3 -2.979506 -4.911603 3
+ 4 -0.867479 -0.910117 4
+ 5 -1.269466 -1.418805 5
+ 6 2.410784 3.762420 6
+ 7 1.766861 2.545012 7
+ 8 1.621663 1.918750 8
+ 9 1.870932 2.278215 9
+ 10 -1.136982 -1.462370 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.383175 0.030542 1
+ 2 -3.758763 -6.119715 2
+ 3 -3.154779 -4.206413 3
+ 4 -0.874583 -0.917208 4
+ 5 -1.387569 -2.096189 5
+ 6 2.602191 3.750634 6
+ 7 1.994254 3.358610 7
+ 8 1.747113 2.499816 8
+ 9 1.915919 2.185842 9
+ 10 -1.282146 -2.153134 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.296543 -0.309884 1
+ 2 -4.141493 -6.820603 2
+ 3 -3.290550 -4.240951 3
+ 4 -0.837652 -0.579136 4
+ 5 -1.491646 -2.220179 5
+ 6 2.688068 3.289207 6
+ 7 2.149365 3.235145 7
+ 8 1.917967 3.113944 8
+ 9 2.038602 2.897379 9
+ 10 -1.468354 -2.771810 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.234442 -0.262361 1
+ 2 -4.548948 -7.808582 2
+ 3 -3.501952 -5.193167 3
+ 4 -0.818965 -0.669467 4
+ 5 -1.579418 -2.281596 5
+ 6 2.854156 4.182861 6
+ 7 2.360190 4.046783 7
+ 8 2.050168 3.107779 8
+ 9 2.134519 2.901856 9
+ 10 -1.691816 -3.479514 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.205729 -0.052695 1
+ 2 -4.971305 -8.772526 2
+ 3 -3.756567 -6.048102 3
+ 4 -0.842988 -1.059199 4
+ 5 -1.697444 -2.759682 5
+ 6 3.054607 4.858669 6
+ 7 2.568698 4.445279 7
+ 8 2.208072 3.629202 8
+ 9 2.266734 3.456672 9
+ 10 -1.877002 -3.543669 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/colvar.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/colvar.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..0670a8d28fbcbe20d416c9f1102922e4dc77d0b0
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/colvar.data.reference
@@ -0,0 +1,24 @@
+#! FIELDS time phi ves1.bias o1.avergradrms o1.avergradmax
+#! SET min_phi -pi
+#! SET max_phi pi
+ 0.000000 -1.238 0.000 0.000 0.000
+ 1.000000 -1.484 0.000 0.000 0.000
+ 2.000000 -1.324 0.000 0.637 0.970
+ 3.000000 -1.334 4.716 0.637 0.970
+ 4.000000 -1.461 4.403 0.659 0.983
+ 5.000000 -1.220 6.371 0.659 0.983
+ 6.000000 -1.388 7.123 0.649 0.961
+ 7.000000 -1.548 7.766 0.649 0.961
+ 8.000000 -1.843 1.066 0.599 0.981
+ 9.000000 -2.242 -3.365 0.599 0.981
+ 10.000000 -1.148 8.387 0.439 0.847
+ 11.000000 -1.758 5.325 0.439 0.847
+ 12.000000 -1.319 12.218 0.523 0.975
+ 13.000000 -2.991 -1.159 0.523 0.975
+ 14.000000 -1.411 13.737 0.475 0.814
+ 15.000000 -2.599 -0.714 0.475 0.814
+ 16.000000 -1.461 14.602 0.451 0.755
+ 17.000000 -1.379 15.945 0.451 0.755
+ 18.000000 -1.677 10.610 0.598 0.988
+ 19.000000 -1.524 16.005 0.598 0.988
+ 20.000000 -1.200 13.955 0.585 0.965
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/combined_gradient.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/combined_gradient.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..fd2741b6458ded2a3525e6ef0197241c4d2b8000
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/combined_gradient.data.reference
@@ -0,0 +1,210 @@
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.219197 1
+ 2 0.970366 2
+ 3 0.884094 3
+ 4 0.421298 4
+ 5 0.590820 5
+ 6 -0.748809 6
+ 7 -0.576392 7
+ 8 -0.715341 8
+ 9 -0.786645 9
+ 10 0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.171909 1
+ 2 0.983056 2
+ 3 0.933040 3
+ 4 0.336620 4
+ 5 0.487305 5
+ 6 -0.852350 6
+ 7 -0.744842 7
+ 8 -0.617866 8
+ 9 -0.723239 9
+ 10 0.615618 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.262244 1
+ 2 0.961187 2
+ 3 0.847758 3
+ 4 0.499637 4
+ 5 0.691487 5
+ 6 -0.669478 6
+ 7 -0.443979 7
+ 8 -0.823233 8
+ 9 -0.885946 9
+ 10 0.195936 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.124979 1
+ 2 0.981351 2
+ 3 0.925470 3
+ 4 -0.250280 4
+ 5 -0.369879 5
+ 6 -0.834186 6
+ 7 -0.714529 7
+ 8 0.469686 8
+ 9 0.531572 9
+ 10 0.580527 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.114667 1
+ 2 0.844969 2
+ 3 0.418592 3
+ 4 -0.156566 4
+ 5 -0.040031 5
+ 6 0.127972 6
+ 7 0.566166 7
+ 8 -0.232733 8
+ 9 -0.526503 9
+ 10 -0.760892 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.032251 1
+ 2 0.975407 2
+ 3 0.902649 3
+ 4 0.059408 4
+ 5 0.059102 5
+ 6 -0.785568 6
+ 7 -0.631437 7
+ 8 0.000738 8
+ 9 0.112546 9
+ 10 0.449365 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.415413 1
+ 2 0.403378 2
+ 3 -0.705190 3
+ 4 0.007091 4
+ 5 0.677384 5
+ 6 0.011786 6
+ 7 -0.813598 7
+ 8 -0.581066 8
+ 9 0.092373 9
+ 10 0.690764 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.340425 1
+ 2 0.700888 2
+ 3 0.034538 3
+ 4 -0.338072 4
+ 5 0.123991 5
+ 6 0.461427 6
+ 7 0.123465 7
+ 8 -0.614128 8
+ 9 -0.711537 9
+ 10 0.618677 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.047522 1
+ 2 0.987979 2
+ 3 0.952216 3
+ 4 0.090331 4
+ 5 0.061417 5
+ 6 -0.893654 6
+ 7 -0.811638 7
+ 8 0.006164 8
+ 9 -0.004477 9
+ 10 0.707703 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.209666 1
+ 2 0.963944 2
+ 3 0.854935 3
+ 4 0.389732 4
+ 5 0.478086 5
+ 6 -0.675807 6
+ 7 -0.398496 7
+ 8 -0.521422 8
+ 9 -0.554816 9
+ 10 0.064155 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/config b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/config
new file mode 100644
index 0000000000000000000000000000000000000000..d9b022c5f95c12fdf3de7e32807e196863eec343
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/config
@@ -0,0 +1,3 @@
+plumed_modules=ves
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro --dump-forces forces --dump-forces-fmt=%10.6f "
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/fes.ves1.iter-10.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/fes.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d50483ac34516d62eac2c7fd2592ae5ef72ba0af
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/fes.ves1.iter-10.data.reference
@@ -0,0 +1,105 @@
+#! FIELDS phi ves1.fes
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET nbins_phi 100
+#! SET periodic_phi true
+ -3.141592654 20.497536200
+ -3.078760801 19.704062923
+ -3.015928947 18.925946415
+ -2.953097094 18.241634172
+ -2.890265241 17.723868121
+ -2.827433388 17.431435858
+ -2.764601535 17.401912078
+ -2.701769682 17.646168907
+ -2.638937829 18.145285307
+ -2.576105976 18.850270868
+ -2.513274123 19.684757617
+ -2.450442270 20.550529614
+ -2.387610417 21.335481149
+ -2.324778564 21.923347445
+ -2.261946711 22.204361318
+ -2.199114858 22.085874739
+ -2.136283004 21.501958062
+ -2.073451151 20.421055959
+ -2.010619298 18.850933268
+ -1.947787445 16.840372909
+ -1.884955592 14.477371479
+ -1.822123739 11.883890368
+ -1.759291886 9.207532462
+ -1.696460033 6.610797784
+ -1.633628180 4.258799067
+ -1.570796327 2.306468659
+ -1.507964474 0.886346801
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+ -1.382300768 0.000000000
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+ -1.256637061 1.879238705
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+ -1.005309649 11.584235793
+ -0.942477796 14.416091724
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+ -0.816814090 19.454444982
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+ 0.251327412 20.260036806
+ 0.314159265 20.919562617
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+ 1.319468915 20.389741461
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+ 2.450442270 20.344168898
+ 2.513274123 20.710953806
+ 2.576105976 21.153976788
+ 2.638937829 21.616891596
+ 2.701769682 22.038150709
+ 2.764601535 22.357816586
+ 2.827433388 22.524426200
+ 2.890265241 22.501166805
+ 2.953097094 22.270674081
+ 3.015928947 21.837889873
+ 3.078760801 21.230604100
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/forces.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/forces.reference
new file mode 100644
index 0000000000000000000000000000000000000000..75ae219e0f6736a9037c0c36631fa4ee84749782
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/forces.reference
@@ -0,0 +1,504 @@
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diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/gradient.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/gradient.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d5ed9cd37331d40602624e78691f857cca92156f
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/gradient.data.reference
@@ -0,0 +1,210 @@
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.219197 -0.219197 1
+ 2 0.970366 0.970366 2
+ 3 0.884094 0.884094 3
+ 4 0.421298 0.421298 4
+ 5 0.590820 0.590820 5
+ 6 -0.748809 -0.748809 6
+ 7 -0.576392 -0.576392 7
+ 8 -0.715341 -0.715341 8
+ 9 -0.786645 -0.786645 9
+ 10 0.381816 0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.171909 -0.171909 1
+ 2 0.983056 0.983056 2
+ 3 0.933040 0.933040 3
+ 4 0.336620 0.336620 4
+ 5 0.487305 0.487305 5
+ 6 -0.852350 -0.852350 6
+ 7 -0.744842 -0.744842 7
+ 8 -0.617866 -0.617866 8
+ 9 -0.723239 -0.723239 9
+ 10 0.615618 0.615618 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.262470 -0.262470 1
+ 2 0.961283 0.961283 2
+ 3 0.849109 0.849109 3
+ 4 0.501037 0.501037 4
+ 5 0.694439 0.694439 5
+ 6 -0.674944 -0.674944 6
+ 7 -0.456423 -0.456423 7
+ 8 -0.826382 -0.826382 8
+ 9 -0.887287 -0.887287 9
+ 10 0.215323 0.215323 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.123003 0.123003 1
+ 2 0.981481 0.981481 2
+ 3 0.927275 0.927275 3
+ 4 -0.236129 -0.236129 4
+ 5 -0.330226 -0.330226 5
+ 6 -0.841343 -0.841343 6
+ 7 -0.729958 -0.729958 7
+ 8 0.397544 0.397544 8
+ 9 0.432305 0.432305 9
+ 10 0.601249 0.601249 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.106083 0.106083 1
+ 2 0.847417 0.847417 2
+ 3 0.444583 0.444583 3
+ 4 -0.113081 -0.113081 4
+ 5 0.025722 0.025722 5
+ 6 0.065616 0.065616 6
+ 7 0.508739 0.508739 7
+ 8 -0.276699 -0.276699 8
+ 9 -0.535793 -0.535793 9
+ 10 -0.746272 -0.746272 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.031729 -0.031729 1
+ 2 0.975444 0.975444 2
+ 3 0.903083 0.903083 3
+ 4 0.058812 0.058812 4
+ 5 0.076991 0.076991 5
+ 6 -0.786761 -0.786761 6
+ 7 -0.632645 -0.632645 7
+ 8 -0.082751 -0.082751 8
+ 9 -0.073628 -0.073628 9
+ 10 0.448875 0.448875 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.414884 0.414884 1
+ 2 0.568606 0.568606 2
+ 3 -0.002782 -0.002782 3
+ 4 0.008683 0.008683 4
+ 5 0.680270 0.680270 5
+ 6 -0.225628 -0.225628 6
+ 7 -0.813633 -0.813633 7
+ 8 -0.581092 -0.581092 8
+ 9 0.007020 0.007020 9
+ 10 0.690771 0.690771 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.373431 0.373431 1
+ 2 0.754956 0.754956 2
+ 3 0.254162 0.254162 3
+ 4 -0.332883 -0.332883 4
+ 5 0.134220 0.134220 5
+ 6 0.026195 0.026195 6
+ 7 -0.171032 -0.171032 7
+ 8 -0.626246 -0.626246 8
+ 9 -0.715567 -0.715567 9
+ 10 0.635181 0.635181 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.042175 -0.042175 1
+ 2 0.988022 0.988022 2
+ 3 0.952455 0.952455 3
+ 4 0.081463 0.081463 4
+ 5 0.115095 0.115095 5
+ 6 -0.894387 -0.894387 6
+ 7 -0.815592 -0.815592 7
+ 8 -0.140542 -0.140542 8
+ 9 -0.155619 -0.155619 9
+ 10 0.718466 0.718466 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.204695 -0.204695 1
+ 2 0.965411 0.965411 2
+ 3 0.866280 0.866280 3
+ 4 0.384645 0.384645 4
+ 5 0.518469 0.518469 5
+ 6 -0.715888 -0.715888 6
+ 7 -0.534349 -0.534349 7
+ 8 -0.591051 -0.591051 8
+ 9 -0.595595 -0.595595 9
+ 10 0.345874 0.345874 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/plumed.dat b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..e97db4661016ebf126fb5d55ad92457367c37e1c
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/plumed.dat
@@ -0,0 +1,47 @@
+# vim:ft=plumed
+
+phi: TORSION ATOMS=5,7,9,15 NOPBC
+
+bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
+
+VES_LINEAR_EXPANSION ...
+ ARG=phi
+ BASIS_FUNCTIONS=bf1
+ LABEL=ves1
+ TEMP=300.0
+ GRID_BINS=100
+... VES_LINEAR_EXPANSION
+
+# NOTE: These parameters do not reflect parameters used in real simulations!
+# This is only for testing!
+#
+
+OPT_AVERAGED_SGD ...
+ BIAS=ves1
+ STRIDE=1000
+ LABEL=o1
+ STEPSIZE=1.0
+ COEFFS_FILE=coeffs.data
+ COEFFS_OUTPUT=1
+ COEFFS_FMT=%12.6f
+ FES_OUTPUT=10
+ BIAS_OUTPUT=10
+ TARGETDIST_AVERAGES_FMT=%12.6f
+ GRADIENT_FILE=gradient.data
+ GRADIENT_OUTPUT=1
+ GRADIENT_FMT=%12.6f
+ COMBINED_GRADIENT_FILE=combined_gradient.data
+ COMBINED_GRADIENT_OUTPUT=1
+ COMBINED_GRADIENT_FMT=%12.6f
+ MONITOR_AVERAGE_GRADIENT
+ MONITOR_AVERAGES_GRADIENT_EXP_DECAY=1
+... OPT_AVERAGED_SGD
+
+PRINT ...
+ STRIDE=500
+ ARG=phi,ves1.bias,o1.*
+ FILE=colvar.data FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/targetdist-averages.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/targetdist-averages.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..b6bf5b55ccca602f2814808f51085a0599e101ab
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/targetdist-averages.data.reference
@@ -0,0 +1,21 @@
+#! FIELDS idx_phi ves1.targetdist_averages index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 1.000000 0
+ 1 0.000000 1
+ 2 0.000000 2
+ 3 0.000000 3
+ 4 0.000000 4
+ 5 0.000000 5
+ 6 0.000000 6
+ 7 0.000000 7
+ 8 0.000000 8
+ 9 0.000000 9
+ 10 0.000000 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/traj.gro b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/traj.gro
new file mode 100644
index 0000000000000000000000000000000000000000..c1c387a0144ec8021b9e5b0453be534f2ca906e2
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad-exp-decay/traj.gro
@@ -0,0 +1,525 @@
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 0.00000
+ 22
+ 1ACE HH31 1 1.474 1.585 1.200
+ 1ACE CH3 2 1.483 1.508 1.277
+ 1ACE HH32 3 1.476 1.561 1.372
+ 1ACE HH33 4 1.578 1.455 1.278
+ 1ACE C 5 1.353 1.428 1.279
+ 1ACE O 6 1.263 1.449 1.357
+ 2ALA N 7 1.343 1.328 1.191
+ 2ALA H 8 1.415 1.321 1.120
+ 2ALA CA 9 1.233 1.239 1.159
+ 2ALA HA 10 1.144 1.302 1.155
+ 2ALA CB 11 1.244 1.182 1.013
+ 2ALA HB1 12 1.341 1.136 0.992
+ 2ALA HB2 13 1.159 1.117 0.994
+ 2ALA HB3 14 1.242 1.265 0.942
+ 2ALA C 15 1.207 1.140 1.271
+ 2ALA O 16 1.214 1.017 1.241
+ 3NME N 17 1.191 1.177 1.398
+ 3NME H 18 1.192 1.275 1.421
+ 3NME CH3 19 1.189 1.086 1.518
+ 3NME HH31 20 1.170 0.983 1.487
+ 3NME HH32 21 1.283 1.087 1.574
+ 3NME HH33 22 1.108 1.127 1.578
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 1.00000
+ 22
+ 1ACE HH31 1 1.480 1.571 1.214
+ 1ACE CH3 2 1.481 1.493 1.289
+ 1ACE HH32 3 1.502 1.528 1.390
+ 1ACE HH33 4 1.551 1.417 1.255
+ 1ACE C 5 1.344 1.432 1.275
+ 1ACE O 6 1.250 1.462 1.345
+ 2ALA N 7 1.342 1.327 1.193
+ 2ALA H 8 1.430 1.313 1.144
+ 2ALA CA 9 1.233 1.244 1.166
+ 2ALA HA 10 1.144 1.307 1.173
+ 2ALA CB 11 1.240 1.189 1.017
+ 2ALA HB1 12 1.327 1.124 1.000
+ 2ALA HB2 13 1.150 1.128 1.005
+ 2ALA HB3 14 1.251 1.267 0.941
+ 2ALA C 15 1.221 1.133 1.271
+ 2ALA O 16 1.217 1.015 1.238
+ 3NME N 17 1.204 1.174 1.395
+ 3NME H 18 1.200 1.275 1.398
+ 3NME CH3 19 1.188 1.089 1.516
+ 3NME HH31 20 1.083 1.086 1.543
+ 3NME HH32 21 1.233 0.990 1.511
+ 3NME HH33 22 1.241 1.141 1.596
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 2.00000
+ 22
+ 1ACE HH31 1 1.532 1.520 1.209
+ 1ACE CH3 2 1.478 1.493 1.300
+ 1ACE HH32 3 1.465 1.586 1.356
+ 1ACE HH33 4 1.548 1.426 1.350
+ 1ACE C 5 1.352 1.423 1.279
+ 1ACE O 6 1.252 1.461 1.340
+ 2ALA N 7 1.351 1.326 1.190
+ 2ALA H 8 1.442 1.293 1.160
+ 2ALA CA 9 1.232 1.244 1.160
+ 2ALA HA 10 1.146 1.310 1.151
+ 2ALA CB 11 1.241 1.190 1.016
+ 2ALA HB1 12 1.333 1.132 1.008
+ 2ALA HB2 13 1.160 1.123 0.986
+ 2ALA HB3 14 1.242 1.280 0.955
+ 2ALA C 15 1.203 1.138 1.270
+ 2ALA O 16 1.161 1.021 1.240
+ 3NME N 17 1.230 1.171 1.396
+ 3NME H 18 1.257 1.266 1.417
+ 3NME CH3 19 1.217 1.090 1.512
+ 3NME HH31 20 1.144 1.011 1.493
+ 3NME HH32 21 1.307 1.029 1.526
+ 3NME HH33 22 1.212 1.146 1.605
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 3.00000
+ 22
+ 1ACE HH31 1 1.439 1.582 1.175
+ 1ACE CH3 2 1.474 1.516 1.254
+ 1ACE HH32 3 1.480 1.585 1.338
+ 1ACE HH33 4 1.569 1.465 1.242
+ 1ACE C 5 1.364 1.419 1.280
+ 1ACE O 6 1.277 1.446 1.367
+ 2ALA N 7 1.358 1.323 1.194
+ 2ALA H 8 1.443 1.313 1.140
+ 2ALA CA 9 1.235 1.243 1.164
+ 2ALA HA 10 1.150 1.310 1.170
+ 2ALA CB 11 1.240 1.197 1.019
+ 2ALA HB1 12 1.316 1.119 1.016
+ 2ALA HB2 13 1.145 1.157 0.982
+ 2ALA HB3 14 1.279 1.276 0.955
+ 2ALA C 15 1.201 1.137 1.272
+ 2ALA O 16 1.172 1.021 1.232
+ 3NME N 17 1.218 1.166 1.402
+ 3NME H 18 1.240 1.259 1.434
+ 3NME CH3 19 1.186 1.086 1.518
+ 3NME HH31 20 1.225 0.984 1.527
+ 3NME HH32 21 1.193 1.134 1.616
+ 3NME HH33 22 1.081 1.058 1.509
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 4.00000
+ 22
+ 1ACE HH31 1 1.549 1.508 1.196
+ 1ACE CH3 2 1.500 1.486 1.290
+ 1ACE HH32 3 1.487 1.571 1.357
+ 1ACE HH33 4 1.563 1.415 1.343
+ 1ACE C 5 1.362 1.425 1.270
+ 1ACE O 6 1.265 1.465 1.340
+ 2ALA N 7 1.349 1.324 1.182
+ 2ALA H 8 1.432 1.287 1.138
+ 2ALA CA 9 1.221 1.249 1.168
+ 2ALA HA 10 1.138 1.318 1.184
+ 2ALA CB 11 1.201 1.194 1.025
+ 2ALA HB1 12 1.276 1.117 1.005
+ 2ALA HB2 13 1.096 1.165 1.014
+ 2ALA HB3 14 1.229 1.265 0.947
+ 2ALA C 15 1.217 1.141 1.275
+ 2ALA O 16 1.234 1.024 1.243
+ 3NME N 17 1.183 1.174 1.400
+ 3NME H 18 1.184 1.274 1.412
+ 3NME CH3 19 1.187 1.078 1.509
+ 3NME HH31 20 1.248 0.990 1.490
+ 3NME HH32 21 1.220 1.120 1.604
+ 3NME HH33 22 1.088 1.035 1.527
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 5.00000
+ 22
+ 1ACE HH31 1 1.449 1.585 1.168
+ 1ACE CH3 2 1.479 1.518 1.248
+ 1ACE HH32 3 1.523 1.577 1.328
+ 1ACE HH33 4 1.565 1.461 1.213
+ 1ACE C 5 1.364 1.422 1.284
+ 1ACE O 6 1.305 1.438 1.389
+ 2ALA N 7 1.347 1.326 1.187
+ 2ALA H 8 1.423 1.328 1.122
+ 2ALA CA 9 1.226 1.241 1.162
+ 2ALA HA 10 1.139 1.308 1.162
+ 2ALA CB 11 1.236 1.193 1.023
+ 2ALA HB1 12 1.314 1.117 1.012
+ 2ALA HB2 13 1.137 1.167 0.986
+ 2ALA HB3 14 1.273 1.278 0.966
+ 2ALA C 15 1.195 1.133 1.268
+ 2ALA O 16 1.173 1.016 1.239
+ 3NME N 17 1.204 1.175 1.393
+ 3NME H 18 1.211 1.275 1.403
+ 3NME CH3 19 1.188 1.090 1.513
+ 3NME HH31 20 1.089 1.044 1.509
+ 3NME HH32 21 1.267 1.014 1.509
+ 3NME HH33 22 1.189 1.145 1.607
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 6.00000
+ 22
+ 1ACE HH31 1 1.517 1.511 1.181
+ 1ACE CH3 2 1.490 1.488 1.284
+ 1ACE HH32 3 1.482 1.582 1.339
+ 1ACE HH33 4 1.569 1.421 1.316
+ 1ACE C 5 1.359 1.414 1.282
+ 1ACE O 6 1.272 1.447 1.358
+ 2ALA N 7 1.351 1.320 1.186
+ 2ALA H 8 1.434 1.297 1.133
+ 2ALA CA 9 1.220 1.251 1.159
+ 2ALA HA 10 1.139 1.323 1.167
+ 2ALA CB 11 1.220 1.194 1.018
+ 2ALA HB1 12 1.298 1.120 1.003
+ 2ALA HB2 13 1.120 1.158 0.994
+ 2ALA HB3 14 1.224 1.286 0.960
+ 2ALA C 15 1.201 1.139 1.270
+ 2ALA O 16 1.190 1.022 1.239
+ 3NME N 17 1.203 1.178 1.393
+ 3NME H 18 1.207 1.277 1.409
+ 3NME CH3 19 1.211 1.102 1.515
+ 3NME HH31 20 1.111 1.064 1.534
+ 3NME HH32 21 1.275 1.017 1.492
+ 3NME HH33 22 1.264 1.151 1.597
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 7.00000
+ 22
+ 1ACE HH31 1 1.483 1.590 1.185
+ 1ACE CH3 2 1.505 1.501 1.245
+ 1ACE HH32 3 1.538 1.533 1.344
+ 1ACE HH33 4 1.580 1.430 1.209
+ 1ACE C 5 1.379 1.418 1.267
+ 1ACE O 6 1.298 1.443 1.349
+ 2ALA N 7 1.360 1.320 1.187
+ 2ALA H 8 1.426 1.297 1.114
+ 2ALA CA 9 1.224 1.253 1.180
+ 2ALA HA 10 1.147 1.326 1.205
+ 2ALA CB 11 1.174 1.215 1.037
+ 2ALA HB1 12 1.245 1.152 0.983
+ 2ALA HB2 13 1.084 1.154 1.032
+ 2ALA HB3 14 1.153 1.311 0.992
+ 2ALA C 15 1.212 1.141 1.280
+ 2ALA O 16 1.219 1.022 1.244
+ 3NME N 17 1.191 1.176 1.408
+ 3NME H 18 1.207 1.275 1.423
+ 3NME CH3 19 1.162 1.068 1.509
+ 3NME HH31 20 1.229 0.982 1.503
+ 3NME HH32 21 1.162 1.109 1.610
+ 3NME HH33 22 1.056 1.044 1.499
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 8.00000
+ 22
+ 1ACE HH31 1 1.576 1.425 1.169
+ 1ACE CH3 2 1.523 1.455 1.260
+ 1ACE HH32 3 1.547 1.556 1.294
+ 1ACE HH33 4 1.566 1.393 1.338
+ 1ACE C 5 1.385 1.422 1.255
+ 1ACE O 6 1.308 1.499 1.305
+ 2ALA N 7 1.346 1.311 1.189
+ 2ALA H 8 1.419 1.248 1.159
+ 2ALA CA 9 1.210 1.260 1.193
+ 2ALA HA 10 1.139 1.326 1.242
+ 2ALA CB 11 1.152 1.252 1.051
+ 2ALA HB1 12 1.230 1.210 0.987
+ 2ALA HB2 13 1.066 1.185 1.052
+ 2ALA HB3 14 1.127 1.354 1.024
+ 2ALA C 15 1.206 1.136 1.282
+ 2ALA O 16 1.195 1.023 1.229
+ 3NME N 17 1.210 1.152 1.420
+ 3NME H 18 1.221 1.243 1.463
+ 3NME CH3 19 1.185 1.048 1.518
+ 3NME HH31 20 1.195 0.948 1.475
+ 3NME HH32 21 1.261 1.070 1.593
+ 3NME HH33 22 1.088 1.064 1.565
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 9.00000
+ 22
+ 1ACE HH31 1 1.515 1.474 1.040
+ 1ACE CH3 2 1.535 1.461 1.147
+ 1ACE HH32 3 1.561 1.560 1.184
+ 1ACE HH33 4 1.612 1.386 1.165
+ 1ACE C 5 1.406 1.430 1.217
+ 1ACE O 6 1.361 1.502 1.307
+ 2ALA N 7 1.345 1.316 1.190
+ 2ALA H 8 1.384 1.254 1.121
+ 2ALA CA 9 1.217 1.277 1.242
+ 2ALA HA 10 1.187 1.348 1.319
+ 2ALA CB 11 1.111 1.278 1.134
+ 2ALA HB1 12 1.129 1.198 1.062
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+ 2ALA HB3 14 1.121 1.372 1.079
+ 2ALA C 15 1.217 1.133 1.309
+ 2ALA O 16 1.293 1.044 1.265
+ 3NME N 17 1.132 1.116 1.408
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+ 3NME CH3 19 1.112 1.003 1.490
+ 3NME HH31 20 1.156 0.910 1.456
+ 3NME HH32 21 1.153 1.026 1.588
+ 3NME HH33 22 1.005 0.985 1.500
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 10.00000
+ 22
+ 1ACE HH31 1 1.536 1.485 1.135
+ 1ACE CH3 2 1.521 1.460 1.240
+ 1ACE HH32 3 1.528 1.557 1.289
+ 1ACE HH33 4 1.602 1.397 1.276
+ 1ACE C 5 1.385 1.401 1.261
+ 1ACE O 6 1.341 1.416 1.373
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+ 2ALA H 8 1.364 1.316 1.076
+ 2ALA CA 9 1.190 1.273 1.177
+ 2ALA HA 10 1.125 1.352 1.216
+ 2ALA CB 11 1.134 1.230 1.038
+ 2ALA HB1 12 1.167 1.128 1.016
+ 2ALA HB2 13 1.026 1.238 1.046
+ 2ALA HB3 14 1.174 1.287 0.953
+ 2ALA C 15 1.183 1.157 1.283
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+ 3NME CH3 19 1.264 1.070 1.510
+ 3NME HH31 20 1.163 1.057 1.548
+ 3NME HH32 21 1.311 0.974 1.487
+ 3NME HH33 22 1.326 1.109 1.592
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 11.00000
+ 22
+ 1ACE HH31 1 1.607 1.359 1.178
+ 1ACE CH3 2 1.535 1.442 1.176
+ 1ACE HH32 3 1.521 1.470 1.072
+ 1ACE HH33 4 1.569 1.533 1.224
+ 1ACE C 5 1.402 1.412 1.242
+ 1ACE O 6 1.368 1.454 1.350
+ 2ALA N 7 1.319 1.332 1.177
+ 2ALA H 8 1.363 1.279 1.103
+ 2ALA CA 9 1.194 1.289 1.231
+ 2ALA HA 10 1.153 1.355 1.308
+ 2ALA CB 11 1.092 1.300 1.113
+ 2ALA HB1 12 1.137 1.243 1.032
+ 2ALA HB2 13 1.001 1.243 1.131
+ 2ALA HB3 14 1.070 1.405 1.095
+ 2ALA C 15 1.198 1.143 1.290
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+ 3NME H 18 1.164 1.213 1.472
+ 3NME CH3 19 1.200 1.009 1.496
+ 3NME HH31 20 1.118 0.938 1.493
+ 3NME HH32 21 1.284 0.953 1.454
+ 3NME HH33 22 1.230 1.031 1.598
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 12.00000
+ 22
+ 1ACE HH31 1 1.491 1.569 1.138
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+ 1ACE HH32 3 1.614 1.449 1.166
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+ 1ACE C 5 1.416 1.394 1.229
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+ 2ALA N 7 1.299 1.357 1.181
+ 2ALA H 8 1.278 1.358 1.082
+ 2ALA CA 9 1.196 1.301 1.267
+ 2ALA HA 10 1.185 1.364 1.355
+ 2ALA CB 11 1.063 1.319 1.182
+ 2ALA HB1 12 1.057 1.248 1.100
+ 2ALA HB2 13 0.976 1.288 1.240
+ 2ALA HB3 14 1.037 1.423 1.161
+ 2ALA C 15 1.226 1.161 1.304
+ 2ALA O 16 1.317 1.094 1.258
+ 3NME N 17 1.135 1.110 1.387
+ 3NME H 18 1.064 1.174 1.419
+ 3NME CH3 19 1.121 0.972 1.429
+ 3NME HH31 20 1.163 0.900 1.358
+ 3NME HH32 21 1.177 0.954 1.520
+ 3NME HH33 22 1.016 0.942 1.428
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 13.00000
+ 22
+ 1ACE HH31 1 1.528 1.537 1.077
+ 1ACE CH3 2 1.543 1.448 1.137
+ 1ACE HH32 3 1.634 1.463 1.195
+ 1ACE HH33 4 1.560 1.362 1.072
+ 1ACE C 5 1.421 1.428 1.229
+ 1ACE O 6 1.396 1.520 1.301
+ 2ALA N 7 1.355 1.314 1.219
+ 2ALA H 8 1.385 1.241 1.156
+ 2ALA CA 9 1.249 1.276 1.311
+ 2ALA HA 10 1.297 1.288 1.409
+ 2ALA CB 11 1.122 1.359 1.284
+ 2ALA HB1 12 1.072 1.325 1.193
+ 2ALA HB2 13 1.053 1.352 1.367
+ 2ALA HB3 14 1.153 1.463 1.275
+ 2ALA C 15 1.204 1.131 1.290
+ 2ALA O 16 1.225 1.070 1.185
+ 3NME N 17 1.131 1.077 1.382
+ 3NME H 18 1.104 1.132 1.463
+ 3NME CH3 19 1.083 0.939 1.380
+ 3NME HH31 20 1.012 0.925 1.298
+ 3NME HH32 21 1.168 0.871 1.372
+ 3NME HH33 22 1.036 0.915 1.475
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 14.00000
+ 22
+ 1ACE HH31 1 1.543 1.468 1.123
+ 1ACE CH3 2 1.548 1.443 1.229
+ 1ACE HH32 3 1.566 1.540 1.276
+ 1ACE HH33 4 1.634 1.382 1.257
+ 1ACE C 5 1.420 1.385 1.285
+ 1ACE O 6 1.412 1.375 1.404
+ 2ALA N 7 1.324 1.361 1.200
+ 2ALA H 8 1.345 1.354 1.101
+ 2ALA CA 9 1.189 1.323 1.244
+ 2ALA HA 10 1.163 1.394 1.323
+ 2ALA CB 11 1.094 1.344 1.125
+ 2ALA HB1 12 1.098 1.270 1.045
+ 2ALA HB2 13 0.995 1.352 1.170
+ 2ALA HB3 14 1.120 1.440 1.079
+ 2ALA C 15 1.166 1.169 1.284
+ 2ALA O 16 1.055 1.145 1.330
+ 3NME N 17 1.263 1.077 1.279
+ 3NME H 18 1.356 1.102 1.247
+ 3NME CH3 19 1.246 0.942 1.335
+ 3NME HH31 20 1.142 0.911 1.345
+ 3NME HH32 21 1.293 0.868 1.270
+ 3NME HH33 22 1.292 0.934 1.434
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 15.00000
+ 22
+ 1ACE HH31 1 1.508 1.417 1.043
+ 1ACE CH3 2 1.539 1.448 1.143
+ 1ACE HH32 3 1.565 1.553 1.146
+ 1ACE HH33 4 1.630 1.395 1.169
+ 1ACE C 5 1.438 1.410 1.253
+ 1ACE O 6 1.429 1.471 1.356
+ 2ALA N 7 1.348 1.327 1.217
+ 2ALA H 8 1.362 1.285 1.126
+ 2ALA CA 9 1.233 1.289 1.298
+ 2ALA HA 10 1.269 1.295 1.401
+ 2ALA CB 11 1.107 1.379 1.286
+ 2ALA HB1 12 1.057 1.360 1.191
+ 2ALA HB2 13 1.034 1.369 1.366
+ 2ALA HB3 14 1.141 1.482 1.282
+ 2ALA C 15 1.192 1.141 1.266
+ 2ALA O 16 1.220 1.089 1.156
+ 3NME N 17 1.131 1.075 1.364
+ 3NME H 18 1.117 1.126 1.450
+ 3NME CH3 19 1.090 0.931 1.376
+ 3NME HH31 20 1.156 0.880 1.446
+ 3NME HH32 21 0.996 0.929 1.431
+ 3NME HH33 22 1.090 0.874 1.283
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 16.00000
+ 22
+ 1ACE HH31 1 1.587 1.386 1.166
+ 1ACE CH3 2 1.554 1.425 1.262
+ 1ACE HH32 3 1.559 1.534 1.266
+ 1ACE HH33 4 1.627 1.390 1.335
+ 1ACE C 5 1.417 1.372 1.300
+ 1ACE O 6 1.390 1.364 1.421
+ 2ALA N 7 1.334 1.344 1.205
+ 2ALA H 8 1.365 1.367 1.111
+ 2ALA CA 9 1.190 1.324 1.235
+ 2ALA HA 10 1.160 1.386 1.319
+ 2ALA CB 11 1.105 1.363 1.112
+ 2ALA HB1 12 1.129 1.297 1.029
+ 2ALA HB2 13 0.999 1.351 1.131
+ 2ALA HB3 14 1.125 1.467 1.088
+ 2ALA C 15 1.162 1.180 1.282
+ 2ALA O 16 1.054 1.128 1.258
+ 3NME N 17 1.261 1.106 1.318
+ 3NME H 18 1.349 1.152 1.336
+ 3NME CH3 19 1.250 0.960 1.324
+ 3NME HH31 20 1.264 0.908 1.229
+ 3NME HH32 21 1.322 0.926 1.399
+ 3NME HH33 22 1.153 0.923 1.357
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 17.00000
+ 22
+ 1ACE HH31 1 1.614 1.382 1.173
+ 1ACE CH3 2 1.559 1.432 1.253
+ 1ACE HH32 3 1.547 1.532 1.213
+ 1ACE HH33 4 1.625 1.444 1.339
+ 1ACE C 5 1.426 1.380 1.288
+ 1ACE O 6 1.411 1.348 1.406
+ 2ALA N 7 1.325 1.370 1.200
+ 2ALA H 8 1.341 1.388 1.102
+ 2ALA CA 9 1.189 1.318 1.239
+ 2ALA HA 10 1.170 1.358 1.338
+ 2ALA CB 11 1.084 1.388 1.158
+ 2ALA HB1 12 1.113 1.369 1.055
+ 2ALA HB2 13 0.994 1.336 1.189
+ 2ALA HB3 14 1.075 1.493 1.186
+ 2ALA C 15 1.170 1.163 1.252
+ 2ALA O 16 1.097 1.103 1.171
+ 3NME N 17 1.235 1.099 1.349
+ 3NME H 18 1.305 1.153 1.399
+ 3NME CH3 19 1.220 0.964 1.393
+ 3NME HH31 20 1.315 0.912 1.406
+ 3NME HH32 21 1.168 0.953 1.489
+ 3NME HH33 22 1.178 0.897 1.318
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 18.00000
+ 22
+ 1ACE HH31 1 1.555 1.419 1.126
+ 1ACE CH3 2 1.554 1.431 1.235
+ 1ACE HH32 3 1.554 1.535 1.267
+ 1ACE HH33 4 1.638 1.381 1.283
+ 1ACE C 5 1.423 1.378 1.292
+ 1ACE O 6 1.416 1.347 1.409
+ 2ALA N 7 1.322 1.351 1.211
+ 2ALA H 8 1.350 1.370 1.115
+ 2ALA CA 9 1.185 1.318 1.251
+ 2ALA HA 10 1.171 1.358 1.352
+ 2ALA CB 11 1.091 1.400 1.149
+ 2ALA HB1 12 1.059 1.346 1.060
+ 2ALA HB2 13 1.008 1.443 1.205
+ 2ALA HB3 14 1.154 1.480 1.109
+ 2ALA C 15 1.163 1.166 1.255
+ 2ALA O 16 1.060 1.108 1.214
+ 3NME N 17 1.255 1.102 1.328
+ 3NME H 18 1.335 1.159 1.354
+ 3NME CH3 19 1.246 0.964 1.369
+ 3NME HH31 20 1.154 0.913 1.344
+ 3NME HH32 21 1.323 0.899 1.327
+ 3NME HH33 22 1.251 0.953 1.477
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 19.00000
+ 22
+ 1ACE HH31 1 1.559 1.326 1.133
+ 1ACE CH3 2 1.552 1.413 1.200
+ 1ACE HH32 3 1.538 1.504 1.142
+ 1ACE HH33 4 1.631 1.428 1.273
+ 1ACE C 5 1.426 1.375 1.280
+ 1ACE O 6 1.428 1.345 1.398
+ 2ALA N 7 1.319 1.363 1.209
+ 2ALA H 8 1.322 1.382 1.110
+ 2ALA CA 9 1.191 1.329 1.265
+ 2ALA HA 10 1.186 1.364 1.368
+ 2ALA CB 11 1.075 1.391 1.178
+ 2ALA HB1 12 1.098 1.383 1.072
+ 2ALA HB2 13 0.980 1.348 1.211
+ 2ALA HB3 14 1.066 1.499 1.192
+ 2ALA C 15 1.169 1.174 1.275
+ 2ALA O 16 1.086 1.118 1.203
+ 3NME N 17 1.233 1.105 1.363
+ 3NME H 18 1.312 1.150 1.405
+ 3NME CH3 19 1.242 0.956 1.350
+ 3NME HH31 20 1.219 0.899 1.440
+ 3NME HH32 21 1.165 0.918 1.284
+ 3NME HH33 22 1.333 0.921 1.301
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 20.00000
+ 22
+ 1ACE HH31 1 1.622 1.459 1.287
+ 1ACE CH3 2 1.546 1.434 1.214
+ 1ACE HH32 3 1.578 1.365 1.135
+ 1ACE HH33 4 1.509 1.531 1.180
+ 1ACE C 5 1.430 1.358 1.283
+ 1ACE O 6 1.444 1.310 1.394
+ 2ALA N 7 1.315 1.370 1.215
+ 2ALA H 8 1.323 1.427 1.132
+ 2ALA CA 9 1.178 1.334 1.258
+ 2ALA HA 10 1.163 1.376 1.357
+ 2ALA CB 11 1.079 1.393 1.158
+ 2ALA HB1 12 1.096 1.348 1.060
+ 2ALA HB2 13 0.979 1.367 1.192
+ 2ALA HB3 14 1.087 1.501 1.165
+ 2ALA C 15 1.163 1.177 1.270
+ 2ALA O 16 1.073 1.114 1.216
+ 3NME N 17 1.249 1.110 1.347
+ 3NME H 18 1.324 1.165 1.388
+ 3NME CH3 19 1.242 0.964 1.360
+ 3NME HH31 20 1.325 0.920 1.416
+ 3NME HH32 21 1.151 0.938 1.414
+ 3NME HH33 22 1.221 0.913 1.266
+ 10.00000 10.00000 10.00000
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/Makefile b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/bias.ves1.iter-10.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/bias.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..55fc4b90e0bb8e0a74059ba4d1ad0bc14e44ef67
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/bias.ves1.iter-10.data.reference
@@ -0,0 +1,105 @@
+#! FIELDS phi ves1.bias der_phi
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET nbins_phi 100
+#! SET periodic_phi true
+ -3.141592654 -1.962887340 -12.338802116
+ -3.078760801 -1.169414064 -12.715200498
+ -3.015928947 -0.391297555 -11.842670932
+ -2.953097094 0.293014687 -9.744489584
+ -2.890265241 0.810780738 -6.578621340
+ -2.827433388 1.103213002 -2.628636251
+ -2.764601535 1.132736781 1.718540218
+ -2.701769682 0.888479952 6.006285748
+ -2.638937829 0.389363553 9.750412598
+ -2.576105976 -0.315622008 12.485919949
+ -2.513274123 -1.150108758 13.813956198
+ -2.450442270 -2.015880754 13.444439030
+ -2.387610417 -2.800832289 11.230078693
+ -2.324778564 -3.388698586 7.188264732
+ -2.261946711 -3.669712459 1.508346390
+ -2.199114858 -3.551225879 -5.456835497
+ -2.136283004 -2.967309202 -13.214845369
+ -2.073451151 -1.886407100 -21.171200499
+ -2.010619298 -0.316284409 -28.677475468
+ -1.947787445 1.694275951 -35.085823711
+ -1.884955592 4.057277381 -39.805102330
+ -1.822123739 6.650758491 -42.353552663
+ -1.759291886 9.327116398 -42.403222481
+ -1.696460033 11.923851076 -39.811998967
+ -1.633628180 14.275849793 -34.640194909
+ -1.570796327 16.228180200 -27.149996573
+ -1.507964474 17.648302059 -17.787615275
+ -1.445132621 18.436646858 -7.149543685
+ -1.382300768 18.534648860 4.064242212
+ -1.319468915 17.929528507 15.106108250
+ -1.256637061 16.655410154 25.240764953
+ -1.193805208 14.790675170 33.804217774
+ -1.130973355 12.451779631 40.256530152
+ -1.068141502 9.784073053 44.223828351
+ -1.005309649 6.950413066 45.525955652
+ -0.942477796 4.118557135 44.187485578
+ -0.879645943 1.448409775 40.431307959
+ -0.816814090 -0.919796122 34.655567695
+ -0.753982237 -2.875401651 27.396218871
+ -0.691150384 -4.344509048 19.278719545
+ -0.628318531 -5.293907399 10.963319829
+ -0.565486678 -5.731488729 3.088904596
+ -0.502654825 -5.703221985 -3.779600964
+ -0.439822972 -5.287056426 -9.195669122
+ -0.376991118 -4.584390419 -12.863688798
+ -0.314159265 -3.709942861 -14.656970625
+ -0.251327412 -2.780984749 -14.620029905
+ -0.188495559 -1.906918090 -12.955414618
+ -0.125663706 -1.180127187 -9.996768596
+ -0.062831853 -0.668881003 -6.171056989
+ 0.000000000 -0.412850137 -1.953818247
+ 0.062831853 -0.421539575 2.178140178
+ 0.125663706 -0.675654705 5.792062628
+ 0.188495559 -1.131140428 8.538354992
+ 0.251327412 -1.725387947 10.179965544
+ 0.314159265 -2.384913757 10.609550868
+ 0.376991118 -3.033697597 9.853189732
+ 0.439822972 -3.601330342 8.060748792
+ 0.502654825 -4.030170819 5.484305244
+ 0.565486678 -4.280835606 2.447166697
+ 0.628318531 -4.335534258 -0.693110509
+ 0.691150384 -4.198993981 -3.583796504
+ 0.753982237 -3.896968936 -5.914139727
+ 0.816814090 -3.472574521 -7.446871847
+ 0.879645943 -2.980902025 -8.041001900
+ 0.942477796 -2.482532833 -7.663790383
+ 1.005309649 -2.036668522 -6.390943538
+ 1.068141502 -1.694615038 -4.395294320
+ 1.130973355 -1.494304801 -1.925415089
+ 1.193805208 -1.456416832 0.723380390
+ 1.256637061 -1.582475512 3.242441860
+ 1.319468915 -1.855092601 5.343983442
+ 1.382300768 -2.240287277 6.792439000
+ 1.445132621 -2.691599109 7.429676026
+ 1.507964474 -3.155521657 7.191454953
+ 1.570796327 -3.577648783 6.113468227
+ 1.633628180 -3.908855525 4.326406440
+ 1.696460033 -4.110837235 2.040661900
+ 1.759291886 -4.160404057 -0.477626840
+ 1.822123739 -4.052064683 -2.936575167
+ 1.884955592 -3.798619184 -5.051347997
+ 1.947787445 -3.429696029 -6.576207401
+ 2.010619298 -2.988390547 -7.332346000
+ 2.073451151 -2.526367898 -7.228480223
+ 2.136283004 -2.097961365 -6.271936183
+ 2.199114858 -1.753908884 -4.568960171
+ 2.261946711 -1.535415076 -2.314123056
+ 2.324778564 -1.469197662 0.230153754
+ 2.387610417 -1.564078476 2.761863469
+ 2.450442270 -1.809520038 4.972532009
+ 2.513274123 -2.176304947 6.581698361
+ 2.576105976 -2.619327928 7.369072046
+ 2.638937829 -3.082242736 7.200869631
+ 2.701769682 -3.503501849 6.047385643
+ 2.764601535 -3.823167726 3.989720592
+ 2.827433388 -3.989777340 1.214684827
+ 2.890265241 -3.966517945 -2.001887206
+ 2.953097094 -3.736025222 -5.321964767
+ 3.015928947 -3.303241013 -8.379756402
+ 3.078760801 -2.695955240 -10.820370974
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/coeffs.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/coeffs.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..478cffec045c1a8bfd01d84cb123d22f99f8168b
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/coeffs.data.reference
@@ -0,0 +1,231 @@
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.000000 0.000000 1
+ 2 0.000000 0.000000 2
+ 3 0.000000 0.000000 3
+ 4 0.000000 0.000000 4
+ 5 0.000000 0.000000 5
+ 6 0.000000 0.000000 6
+ 7 0.000000 0.000000 7
+ 8 0.000000 0.000000 8
+ 9 0.000000 0.000000 9
+ 10 0.000000 0.000000 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.219197 0.219197 1
+ 2 -0.970366 -0.970366 2
+ 3 -0.884094 -0.884094 3
+ 4 -0.421298 -0.421298 4
+ 5 -0.590820 -0.590820 5
+ 6 0.748809 0.748809 6
+ 7 0.576392 0.576392 7
+ 8 0.715341 0.715341 8
+ 9 0.786645 0.786645 9
+ 10 -0.381816 -0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.305152 0.391107 1
+ 2 -1.461895 -1.953423 2
+ 3 -1.350614 -1.817134 3
+ 4 -0.589608 -0.757918 4
+ 5 -0.834473 -1.078125 5
+ 6 1.174985 1.601160 6
+ 7 0.948813 1.321234 7
+ 8 1.024273 1.333206 8
+ 9 1.148264 1.509884 9
+ 10 -0.689625 -0.997434 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.421218 0.653351 1
+ 2 -1.946133 -2.914610 2
+ 3 -1.788707 -2.664892 3
+ 4 -0.812257 -1.257555 4
+ 5 -1.146186 -1.769612 5
+ 6 1.540202 2.270638 6
+ 7 1.220946 1.765213 7
+ 8 1.401662 2.156440 8
+ 9 1.564119 2.395830 9
+ 10 -0.857540 -1.193370 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.448007 0.528372 1
+ 2 -2.433590 -3.895961 2
+ 3 -2.239120 -3.590362 3
+ 4 -0.861012 -1.007276 4
+ 5 -1.209573 -1.399733 5
+ 6 1.931358 3.104824 6
+ 7 1.535645 2.479741 7
+ 8 1.472935 1.686754 8
+ 9 1.639154 1.864258 9
+ 10 -1.086629 -1.773897 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.441146 0.413704 1
+ 2 -2.895058 -4.740930 2
+ 3 -2.593087 -4.008954 3
+ 4 -0.858951 -0.850710 4
+ 5 -1.239599 -1.359702 5
+ 6 2.140456 2.976852 6
+ 7 1.611231 1.913575 7
+ 8 1.562246 1.919487 8
+ 9 1.789475 2.390761 9
+ 10 -1.071904 -1.013004 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.441948 0.445955 1
+ 2 -3.365271 -5.716337 2
+ 3 -2.979506 -4.911603 3
+ 4 -0.867479 -0.910117 4
+ 5 -1.269466 -1.418805 5
+ 6 2.410784 3.762420 6
+ 7 1.766861 2.545012 7
+ 8 1.621663 1.918750 8
+ 9 1.870932 2.278215 9
+ 10 -1.136982 -1.462370 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.383175 0.030542 1
+ 2 -3.758763 -6.119715 2
+ 3 -3.154779 -4.206413 3
+ 4 -0.874583 -0.917208 4
+ 5 -1.387569 -2.096189 5
+ 6 2.602191 3.750634 6
+ 7 1.994254 3.358610 7
+ 8 1.747113 2.499816 8
+ 9 1.915919 2.185842 9
+ 10 -1.282146 -2.153134 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.296543 -0.309884 1
+ 2 -4.141493 -6.820603 2
+ 3 -3.290550 -4.240951 3
+ 4 -0.837652 -0.579136 4
+ 5 -1.491646 -2.220179 5
+ 6 2.688068 3.289207 6
+ 7 2.149365 3.235145 7
+ 8 1.917967 3.113944 8
+ 9 2.038602 2.897379 9
+ 10 -1.468354 -2.771810 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.234442 -0.262361 1
+ 2 -4.548948 -7.808582 2
+ 3 -3.501952 -5.193167 3
+ 4 -0.818965 -0.669467 4
+ 5 -1.579418 -2.281596 5
+ 6 2.854156 4.182861 6
+ 7 2.360190 4.046783 7
+ 8 2.050168 3.107779 8
+ 9 2.134519 2.901856 9
+ 10 -1.691816 -3.479514 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.205729 -0.052695 1
+ 2 -4.971305 -8.772526 2
+ 3 -3.756567 -6.048102 3
+ 4 -0.842988 -1.059199 4
+ 5 -1.697444 -2.759682 5
+ 6 3.054607 4.858669 6
+ 7 2.568698 4.445279 7
+ 8 2.208072 3.629202 8
+ 9 2.266734 3.456672 9
+ 10 -1.877002 -3.543669 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/colvar.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/colvar.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..7bea698e93ba38c1b40ba7d43f179a7fd123e164
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/colvar.data.reference
@@ -0,0 +1,24 @@
+#! FIELDS time phi ves1.bias o1.avergradrms o1.avergradmax
+#! SET min_phi -pi
+#! SET max_phi pi
+ 0.000000 -1.238 0.000 0.000 0.000
+ 1.000000 -1.484 0.000 0.000 0.000
+ 2.000000 -1.324 0.000 0.637 0.970
+ 3.000000 -1.334 4.716 0.637 0.970
+ 4.000000 -1.461 4.403 0.646 0.977
+ 5.000000 -1.220 6.371 0.646 0.977
+ 6.000000 -1.388 7.123 0.643 0.972
+ 7.000000 -1.548 7.766 0.643 0.972
+ 8.000000 -1.843 1.066 0.573 0.974
+ 9.000000 -2.242 -3.365 0.573 0.974
+ 10.000000 -1.148 8.387 0.493 0.949
+ 11.000000 -1.758 5.325 0.493 0.949
+ 12.000000 -1.319 12.218 0.492 0.953
+ 13.000000 -2.991 -1.159 0.492 0.953
+ 14.000000 -1.411 13.737 0.466 0.898
+ 15.000000 -2.599 -0.714 0.466 0.898
+ 16.000000 -1.461 14.602 0.449 0.880
+ 17.000000 -1.379 15.945 0.449 0.880
+ 18.000000 -1.677 10.610 0.461 0.892
+ 19.000000 -1.524 16.005 0.461 0.892
+ 20.000000 -1.200 13.955 0.472 0.900
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/combined_gradient.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/combined_gradient.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..fd2741b6458ded2a3525e6ef0197241c4d2b8000
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/combined_gradient.data.reference
@@ -0,0 +1,210 @@
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.219197 1
+ 2 0.970366 2
+ 3 0.884094 3
+ 4 0.421298 4
+ 5 0.590820 5
+ 6 -0.748809 6
+ 7 -0.576392 7
+ 8 -0.715341 8
+ 9 -0.786645 9
+ 10 0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.171909 1
+ 2 0.983056 2
+ 3 0.933040 3
+ 4 0.336620 4
+ 5 0.487305 5
+ 6 -0.852350 6
+ 7 -0.744842 7
+ 8 -0.617866 8
+ 9 -0.723239 9
+ 10 0.615618 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.262244 1
+ 2 0.961187 2
+ 3 0.847758 3
+ 4 0.499637 4
+ 5 0.691487 5
+ 6 -0.669478 6
+ 7 -0.443979 7
+ 8 -0.823233 8
+ 9 -0.885946 9
+ 10 0.195936 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.124979 1
+ 2 0.981351 2
+ 3 0.925470 3
+ 4 -0.250280 4
+ 5 -0.369879 5
+ 6 -0.834186 6
+ 7 -0.714529 7
+ 8 0.469686 8
+ 9 0.531572 9
+ 10 0.580527 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.114667 1
+ 2 0.844969 2
+ 3 0.418592 3
+ 4 -0.156566 4
+ 5 -0.040031 5
+ 6 0.127972 6
+ 7 0.566166 7
+ 8 -0.232733 8
+ 9 -0.526503 9
+ 10 -0.760892 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.032251 1
+ 2 0.975407 2
+ 3 0.902649 3
+ 4 0.059408 4
+ 5 0.059102 5
+ 6 -0.785568 6
+ 7 -0.631437 7
+ 8 0.000738 8
+ 9 0.112546 9
+ 10 0.449365 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.415413 1
+ 2 0.403378 2
+ 3 -0.705190 3
+ 4 0.007091 4
+ 5 0.677384 5
+ 6 0.011786 6
+ 7 -0.813598 7
+ 8 -0.581066 8
+ 9 0.092373 9
+ 10 0.690764 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.340425 1
+ 2 0.700888 2
+ 3 0.034538 3
+ 4 -0.338072 4
+ 5 0.123991 5
+ 6 0.461427 6
+ 7 0.123465 7
+ 8 -0.614128 8
+ 9 -0.711537 9
+ 10 0.618677 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.047522 1
+ 2 0.987979 2
+ 3 0.952216 3
+ 4 0.090331 4
+ 5 0.061417 5
+ 6 -0.893654 6
+ 7 -0.811638 7
+ 8 0.006164 8
+ 9 -0.004477 9
+ 10 0.707703 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.209666 1
+ 2 0.963944 2
+ 3 0.854935 3
+ 4 0.389732 4
+ 5 0.478086 5
+ 6 -0.675807 6
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+ 8 -0.521422 8
+ 9 -0.554816 9
+ 10 0.064155 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/config b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/config
new file mode 100644
index 0000000000000000000000000000000000000000..d9b022c5f95c12fdf3de7e32807e196863eec343
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/config
@@ -0,0 +1,3 @@
+plumed_modules=ves
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro --dump-forces forces --dump-forces-fmt=%10.6f "
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/fes.ves1.iter-10.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/fes.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d50483ac34516d62eac2c7fd2592ae5ef72ba0af
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/fes.ves1.iter-10.data.reference
@@ -0,0 +1,105 @@
+#! FIELDS phi ves1.fes
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET nbins_phi 100
+#! SET periodic_phi true
+ -3.141592654 20.497536200
+ -3.078760801 19.704062923
+ -3.015928947 18.925946415
+ -2.953097094 18.241634172
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+ -2.827433388 17.431435858
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+ -2.638937829 18.145285307
+ -2.576105976 18.850270868
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+ 2.450442270 20.344168898
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+ 2.576105976 21.153976788
+ 2.638937829 21.616891596
+ 2.701769682 22.038150709
+ 2.764601535 22.357816586
+ 2.827433388 22.524426200
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+ 2.953097094 22.270674081
+ 3.015928947 21.837889873
+ 3.078760801 21.230604100
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/forces.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/forces.reference
new file mode 100644
index 0000000000000000000000000000000000000000..75ae219e0f6736a9037c0c36631fa4ee84749782
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/forces.reference
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diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/gradient.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/gradient.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..48996868f0db0186cdff3040621b6e3d0e025e8f
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/gradient.data.reference
@@ -0,0 +1,210 @@
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.219197 -0.219197 1
+ 2 0.970366 0.970366 2
+ 3 0.884094 0.884094 3
+ 4 0.421298 0.421298 4
+ 5 0.590820 0.590820 5
+ 6 -0.748809 -0.748809 6
+ 7 -0.576392 -0.576392 7
+ 8 -0.715341 -0.715341 8
+ 9 -0.786645 -0.786645 9
+ 10 0.381816 0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.171909 -0.195553 1
+ 2 0.983056 0.976711 2
+ 3 0.933040 0.908567 3
+ 4 0.336620 0.378959 4
+ 5 0.487305 0.539063 5
+ 6 -0.852350 -0.800580 6
+ 7 -0.744842 -0.660617 7
+ 8 -0.617866 -0.666603 8
+ 9 -0.723239 -0.754942 9
+ 10 0.615618 0.498717 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.262470 -0.217859 1
+ 2 0.961283 0.971569 2
+ 3 0.849109 0.888748 3
+ 4 0.501037 0.419652 4
+ 5 0.694439 0.590855 5
+ 6 -0.674944 -0.758701 6
+ 7 -0.456423 -0.592552 7
+ 8 -0.826382 -0.719863 8
+ 9 -0.887287 -0.799057 9
+ 10 0.215323 0.404252 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.123003 -0.132643 1
+ 2 0.981481 0.974047 2
+ 3 0.927275 0.898380 3
+ 4 -0.236129 0.255707 4
+ 5 -0.330226 0.360584 5
+ 6 -0.841343 -0.779362 6
+ 7 -0.729958 -0.626904 7
+ 8 0.397544 -0.440511 8
+ 9 0.432305 -0.491216 9
+ 10 0.601249 0.453501 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.106083 -0.084898 1
+ 2 0.847417 0.948721 2
+ 3 0.444583 0.807620 3
+ 4 -0.113081 0.181949 4
+ 5 0.025722 0.293612 5
+ 6 0.065616 -0.610366 6
+ 7 0.508739 -0.399775 7
+ 8 -0.276699 -0.407749 8
+ 9 -0.535793 -0.500132 9
+ 10 -0.746272 0.213547 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.031729 -0.076037 1
+ 2 0.975444 0.953175 2
+ 3 0.903083 0.823531 3
+ 4 0.058812 0.161426 4
+ 5 0.076991 0.257509 5
+ 6 -0.786761 -0.639765 6
+ 7 -0.632645 -0.438587 7
+ 8 -0.082751 -0.353583 8
+ 9 -0.073628 -0.429048 9
+ 10 0.448875 0.252768 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.414884 -0.005905 1
+ 2 0.568606 0.898236 2
+ 3 -0.002782 0.705486 3
+ 4 0.008683 0.139606 4
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+ 6 -0.225628 -0.580603 6
+ 7 -0.813633 -0.492165 7
+ 8 -0.581092 -0.386084 8
+ 9 0.007020 -0.366752 9
+ 10 0.690771 0.315340 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.373431 0.041512 1
+ 2 0.754956 0.880326 2
+ 3 0.254162 0.649070 3
+ 4 -0.332883 0.080545 4
+ 5 0.134220 0.294943 5
+ 6 0.026195 -0.504753 6
+ 7 -0.171032 -0.452023 7
+ 8 -0.626246 -0.416104 8
+ 9 -0.715567 -0.410354 9
+ 10 0.635181 0.355320 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.042175 0.032213 1
+ 2 0.988022 0.892292 2
+ 3 0.952455 0.682780 3
+ 4 0.081463 0.080647 4
+ 5 0.115095 0.274959 5
+ 6 -0.894387 -0.548046 6
+ 7 -0.815592 -0.492420 7
+ 8 -0.140542 -0.385486 8
+ 9 -0.155619 -0.382050 9
+ 10 0.718466 0.395670 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.gradient ves1.aver_gradient index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 -0.204695 0.008523 1
+ 2 0.965411 0.899604 2
+ 3 0.866280 0.701130 3
+ 4 0.384645 0.111047 4
+ 5 0.518469 0.299310 5
+ 6 -0.715888 -0.564830 6
+ 7 -0.534349 -0.496613 7
+ 8 -0.591051 -0.406043 8
+ 9 -0.595595 -0.403405 9
+ 10 0.345874 0.390690 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/plumed.dat b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..f65539b1cfc3c54bfc7c534c04e3b9171908684f
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/plumed.dat
@@ -0,0 +1,46 @@
+# vim:ft=plumed
+
+phi: TORSION ATOMS=5,7,9,15 NOPBC
+
+bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
+
+VES_LINEAR_EXPANSION ...
+ ARG=phi
+ BASIS_FUNCTIONS=bf1
+ LABEL=ves1
+ TEMP=300.0
+ GRID_BINS=100
+... VES_LINEAR_EXPANSION
+
+# NOTE: These parameters do not reflect parameters used in real simulations!
+# This is only for testing!
+#
+
+OPT_AVERAGED_SGD ...
+ BIAS=ves1
+ STRIDE=1000
+ LABEL=o1
+ STEPSIZE=1.0
+ COEFFS_FILE=coeffs.data
+ COEFFS_OUTPUT=1
+ COEFFS_FMT=%12.6f
+ FES_OUTPUT=10
+ BIAS_OUTPUT=10
+ TARGETDIST_AVERAGES_FMT=%12.6f
+ GRADIENT_FILE=gradient.data
+ GRADIENT_OUTPUT=1
+ GRADIENT_FMT=%12.6f
+ COMBINED_GRADIENT_FILE=combined_gradient.data
+ COMBINED_GRADIENT_OUTPUT=1
+ COMBINED_GRADIENT_FMT=%12.6f
+ MONITOR_AVERAGE_GRADIENT
+... OPT_AVERAGED_SGD
+
+PRINT ...
+ STRIDE=500
+ ARG=phi,ves1.bias,o1.*
+ FILE=colvar.data FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/targetdist-averages.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/targetdist-averages.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..b6bf5b55ccca602f2814808f51085a0599e101ab
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/targetdist-averages.data.reference
@@ -0,0 +1,21 @@
+#! FIELDS idx_phi ves1.targetdist_averages index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 1.000000 0
+ 1 0.000000 1
+ 2 0.000000 2
+ 3 0.000000 3
+ 4 0.000000 4
+ 5 0.000000 5
+ 6 0.000000 6
+ 7 0.000000 7
+ 8 0.000000 8
+ 9 0.000000 9
+ 10 0.000000 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/traj.gro b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/traj.gro
new file mode 100644
index 0000000000000000000000000000000000000000..c1c387a0144ec8021b9e5b0453be534f2ca906e2
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-aver-grad/traj.gro
@@ -0,0 +1,525 @@
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+ 1ACE C 5 1.362 1.425 1.270
+ 1ACE O 6 1.265 1.465 1.340
+ 2ALA N 7 1.349 1.324 1.182
+ 2ALA H 8 1.432 1.287 1.138
+ 2ALA CA 9 1.221 1.249 1.168
+ 2ALA HA 10 1.138 1.318 1.184
+ 2ALA CB 11 1.201 1.194 1.025
+ 2ALA HB1 12 1.276 1.117 1.005
+ 2ALA HB2 13 1.096 1.165 1.014
+ 2ALA HB3 14 1.229 1.265 0.947
+ 2ALA C 15 1.217 1.141 1.275
+ 2ALA O 16 1.234 1.024 1.243
+ 3NME N 17 1.183 1.174 1.400
+ 3NME H 18 1.184 1.274 1.412
+ 3NME CH3 19 1.187 1.078 1.509
+ 3NME HH31 20 1.248 0.990 1.490
+ 3NME HH32 21 1.220 1.120 1.604
+ 3NME HH33 22 1.088 1.035 1.527
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 5.00000
+ 22
+ 1ACE HH31 1 1.449 1.585 1.168
+ 1ACE CH3 2 1.479 1.518 1.248
+ 1ACE HH32 3 1.523 1.577 1.328
+ 1ACE HH33 4 1.565 1.461 1.213
+ 1ACE C 5 1.364 1.422 1.284
+ 1ACE O 6 1.305 1.438 1.389
+ 2ALA N 7 1.347 1.326 1.187
+ 2ALA H 8 1.423 1.328 1.122
+ 2ALA CA 9 1.226 1.241 1.162
+ 2ALA HA 10 1.139 1.308 1.162
+ 2ALA CB 11 1.236 1.193 1.023
+ 2ALA HB1 12 1.314 1.117 1.012
+ 2ALA HB2 13 1.137 1.167 0.986
+ 2ALA HB3 14 1.273 1.278 0.966
+ 2ALA C 15 1.195 1.133 1.268
+ 2ALA O 16 1.173 1.016 1.239
+ 3NME N 17 1.204 1.175 1.393
+ 3NME H 18 1.211 1.275 1.403
+ 3NME CH3 19 1.188 1.090 1.513
+ 3NME HH31 20 1.089 1.044 1.509
+ 3NME HH32 21 1.267 1.014 1.509
+ 3NME HH33 22 1.189 1.145 1.607
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 6.00000
+ 22
+ 1ACE HH31 1 1.517 1.511 1.181
+ 1ACE CH3 2 1.490 1.488 1.284
+ 1ACE HH32 3 1.482 1.582 1.339
+ 1ACE HH33 4 1.569 1.421 1.316
+ 1ACE C 5 1.359 1.414 1.282
+ 1ACE O 6 1.272 1.447 1.358
+ 2ALA N 7 1.351 1.320 1.186
+ 2ALA H 8 1.434 1.297 1.133
+ 2ALA CA 9 1.220 1.251 1.159
+ 2ALA HA 10 1.139 1.323 1.167
+ 2ALA CB 11 1.220 1.194 1.018
+ 2ALA HB1 12 1.298 1.120 1.003
+ 2ALA HB2 13 1.120 1.158 0.994
+ 2ALA HB3 14 1.224 1.286 0.960
+ 2ALA C 15 1.201 1.139 1.270
+ 2ALA O 16 1.190 1.022 1.239
+ 3NME N 17 1.203 1.178 1.393
+ 3NME H 18 1.207 1.277 1.409
+ 3NME CH3 19 1.211 1.102 1.515
+ 3NME HH31 20 1.111 1.064 1.534
+ 3NME HH32 21 1.275 1.017 1.492
+ 3NME HH33 22 1.264 1.151 1.597
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 7.00000
+ 22
+ 1ACE HH31 1 1.483 1.590 1.185
+ 1ACE CH3 2 1.505 1.501 1.245
+ 1ACE HH32 3 1.538 1.533 1.344
+ 1ACE HH33 4 1.580 1.430 1.209
+ 1ACE C 5 1.379 1.418 1.267
+ 1ACE O 6 1.298 1.443 1.349
+ 2ALA N 7 1.360 1.320 1.187
+ 2ALA H 8 1.426 1.297 1.114
+ 2ALA CA 9 1.224 1.253 1.180
+ 2ALA HA 10 1.147 1.326 1.205
+ 2ALA CB 11 1.174 1.215 1.037
+ 2ALA HB1 12 1.245 1.152 0.983
+ 2ALA HB2 13 1.084 1.154 1.032
+ 2ALA HB3 14 1.153 1.311 0.992
+ 2ALA C 15 1.212 1.141 1.280
+ 2ALA O 16 1.219 1.022 1.244
+ 3NME N 17 1.191 1.176 1.408
+ 3NME H 18 1.207 1.275 1.423
+ 3NME CH3 19 1.162 1.068 1.509
+ 3NME HH31 20 1.229 0.982 1.503
+ 3NME HH32 21 1.162 1.109 1.610
+ 3NME HH33 22 1.056 1.044 1.499
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 8.00000
+ 22
+ 1ACE HH31 1 1.576 1.425 1.169
+ 1ACE CH3 2 1.523 1.455 1.260
+ 1ACE HH32 3 1.547 1.556 1.294
+ 1ACE HH33 4 1.566 1.393 1.338
+ 1ACE C 5 1.385 1.422 1.255
+ 1ACE O 6 1.308 1.499 1.305
+ 2ALA N 7 1.346 1.311 1.189
+ 2ALA H 8 1.419 1.248 1.159
+ 2ALA CA 9 1.210 1.260 1.193
+ 2ALA HA 10 1.139 1.326 1.242
+ 2ALA CB 11 1.152 1.252 1.051
+ 2ALA HB1 12 1.230 1.210 0.987
+ 2ALA HB2 13 1.066 1.185 1.052
+ 2ALA HB3 14 1.127 1.354 1.024
+ 2ALA C 15 1.206 1.136 1.282
+ 2ALA O 16 1.195 1.023 1.229
+ 3NME N 17 1.210 1.152 1.420
+ 3NME H 18 1.221 1.243 1.463
+ 3NME CH3 19 1.185 1.048 1.518
+ 3NME HH31 20 1.195 0.948 1.475
+ 3NME HH32 21 1.261 1.070 1.593
+ 3NME HH33 22 1.088 1.064 1.565
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 9.00000
+ 22
+ 1ACE HH31 1 1.515 1.474 1.040
+ 1ACE CH3 2 1.535 1.461 1.147
+ 1ACE HH32 3 1.561 1.560 1.184
+ 1ACE HH33 4 1.612 1.386 1.165
+ 1ACE C 5 1.406 1.430 1.217
+ 1ACE O 6 1.361 1.502 1.307
+ 2ALA N 7 1.345 1.316 1.190
+ 2ALA H 8 1.384 1.254 1.121
+ 2ALA CA 9 1.217 1.277 1.242
+ 2ALA HA 10 1.187 1.348 1.319
+ 2ALA CB 11 1.111 1.278 1.134
+ 2ALA HB1 12 1.129 1.198 1.062
+ 2ALA HB2 13 1.018 1.269 1.189
+ 2ALA HB3 14 1.121 1.372 1.079
+ 2ALA C 15 1.217 1.133 1.309
+ 2ALA O 16 1.293 1.044 1.265
+ 3NME N 17 1.132 1.116 1.408
+ 3NME H 18 1.076 1.195 1.437
+ 3NME CH3 19 1.112 1.003 1.490
+ 3NME HH31 20 1.156 0.910 1.456
+ 3NME HH32 21 1.153 1.026 1.588
+ 3NME HH33 22 1.005 0.985 1.500
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 10.00000
+ 22
+ 1ACE HH31 1 1.536 1.485 1.135
+ 1ACE CH3 2 1.521 1.460 1.240
+ 1ACE HH32 3 1.528 1.557 1.289
+ 1ACE HH33 4 1.602 1.397 1.276
+ 1ACE C 5 1.385 1.401 1.261
+ 1ACE O 6 1.341 1.416 1.373
+ 2ALA N 7 1.322 1.332 1.167
+ 2ALA H 8 1.364 1.316 1.076
+ 2ALA CA 9 1.190 1.273 1.177
+ 2ALA HA 10 1.125 1.352 1.216
+ 2ALA CB 11 1.134 1.230 1.038
+ 2ALA HB1 12 1.167 1.128 1.016
+ 2ALA HB2 13 1.026 1.238 1.046
+ 2ALA HB3 14 1.174 1.287 0.953
+ 2ALA C 15 1.183 1.157 1.283
+ 2ALA O 16 1.111 1.061 1.259
+ 3NME N 17 1.264 1.157 1.396
+ 3NME H 18 1.320 1.241 1.405
+ 3NME CH3 19 1.264 1.070 1.510
+ 3NME HH31 20 1.163 1.057 1.548
+ 3NME HH32 21 1.311 0.974 1.487
+ 3NME HH33 22 1.326 1.109 1.592
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 11.00000
+ 22
+ 1ACE HH31 1 1.607 1.359 1.178
+ 1ACE CH3 2 1.535 1.442 1.176
+ 1ACE HH32 3 1.521 1.470 1.072
+ 1ACE HH33 4 1.569 1.533 1.224
+ 1ACE C 5 1.402 1.412 1.242
+ 1ACE O 6 1.368 1.454 1.350
+ 2ALA N 7 1.319 1.332 1.177
+ 2ALA H 8 1.363 1.279 1.103
+ 2ALA CA 9 1.194 1.289 1.231
+ 2ALA HA 10 1.153 1.355 1.308
+ 2ALA CB 11 1.092 1.300 1.113
+ 2ALA HB1 12 1.137 1.243 1.032
+ 2ALA HB2 13 1.001 1.243 1.131
+ 2ALA HB3 14 1.070 1.405 1.095
+ 2ALA C 15 1.198 1.143 1.290
+ 2ALA O 16 1.237 1.057 1.213
+ 3NME N 17 1.171 1.126 1.422
+ 3NME H 18 1.164 1.213 1.472
+ 3NME CH3 19 1.200 1.009 1.496
+ 3NME HH31 20 1.118 0.938 1.493
+ 3NME HH32 21 1.284 0.953 1.454
+ 3NME HH33 22 1.230 1.031 1.598
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 12.00000
+ 22
+ 1ACE HH31 1 1.491 1.569 1.138
+ 1ACE CH3 2 1.511 1.462 1.134
+ 1ACE HH32 3 1.614 1.449 1.166
+ 1ACE HH33 4 1.495 1.444 1.028
+ 1ACE C 5 1.416 1.394 1.229
+ 1ACE O 6 1.445 1.392 1.345
+ 2ALA N 7 1.299 1.357 1.181
+ 2ALA H 8 1.278 1.358 1.082
+ 2ALA CA 9 1.196 1.301 1.267
+ 2ALA HA 10 1.185 1.364 1.355
+ 2ALA CB 11 1.063 1.319 1.182
+ 2ALA HB1 12 1.057 1.248 1.100
+ 2ALA HB2 13 0.976 1.288 1.240
+ 2ALA HB3 14 1.037 1.423 1.161
+ 2ALA C 15 1.226 1.161 1.304
+ 2ALA O 16 1.317 1.094 1.258
+ 3NME N 17 1.135 1.110 1.387
+ 3NME H 18 1.064 1.174 1.419
+ 3NME CH3 19 1.121 0.972 1.429
+ 3NME HH31 20 1.163 0.900 1.358
+ 3NME HH32 21 1.177 0.954 1.520
+ 3NME HH33 22 1.016 0.942 1.428
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 13.00000
+ 22
+ 1ACE HH31 1 1.528 1.537 1.077
+ 1ACE CH3 2 1.543 1.448 1.137
+ 1ACE HH32 3 1.634 1.463 1.195
+ 1ACE HH33 4 1.560 1.362 1.072
+ 1ACE C 5 1.421 1.428 1.229
+ 1ACE O 6 1.396 1.520 1.301
+ 2ALA N 7 1.355 1.314 1.219
+ 2ALA H 8 1.385 1.241 1.156
+ 2ALA CA 9 1.249 1.276 1.311
+ 2ALA HA 10 1.297 1.288 1.409
+ 2ALA CB 11 1.122 1.359 1.284
+ 2ALA HB1 12 1.072 1.325 1.193
+ 2ALA HB2 13 1.053 1.352 1.367
+ 2ALA HB3 14 1.153 1.463 1.275
+ 2ALA C 15 1.204 1.131 1.290
+ 2ALA O 16 1.225 1.070 1.185
+ 3NME N 17 1.131 1.077 1.382
+ 3NME H 18 1.104 1.132 1.463
+ 3NME CH3 19 1.083 0.939 1.380
+ 3NME HH31 20 1.012 0.925 1.298
+ 3NME HH32 21 1.168 0.871 1.372
+ 3NME HH33 22 1.036 0.915 1.475
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 14.00000
+ 22
+ 1ACE HH31 1 1.543 1.468 1.123
+ 1ACE CH3 2 1.548 1.443 1.229
+ 1ACE HH32 3 1.566 1.540 1.276
+ 1ACE HH33 4 1.634 1.382 1.257
+ 1ACE C 5 1.420 1.385 1.285
+ 1ACE O 6 1.412 1.375 1.404
+ 2ALA N 7 1.324 1.361 1.200
+ 2ALA H 8 1.345 1.354 1.101
+ 2ALA CA 9 1.189 1.323 1.244
+ 2ALA HA 10 1.163 1.394 1.323
+ 2ALA CB 11 1.094 1.344 1.125
+ 2ALA HB1 12 1.098 1.270 1.045
+ 2ALA HB2 13 0.995 1.352 1.170
+ 2ALA HB3 14 1.120 1.440 1.079
+ 2ALA C 15 1.166 1.169 1.284
+ 2ALA O 16 1.055 1.145 1.330
+ 3NME N 17 1.263 1.077 1.279
+ 3NME H 18 1.356 1.102 1.247
+ 3NME CH3 19 1.246 0.942 1.335
+ 3NME HH31 20 1.142 0.911 1.345
+ 3NME HH32 21 1.293 0.868 1.270
+ 3NME HH33 22 1.292 0.934 1.434
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 15.00000
+ 22
+ 1ACE HH31 1 1.508 1.417 1.043
+ 1ACE CH3 2 1.539 1.448 1.143
+ 1ACE HH32 3 1.565 1.553 1.146
+ 1ACE HH33 4 1.630 1.395 1.169
+ 1ACE C 5 1.438 1.410 1.253
+ 1ACE O 6 1.429 1.471 1.356
+ 2ALA N 7 1.348 1.327 1.217
+ 2ALA H 8 1.362 1.285 1.126
+ 2ALA CA 9 1.233 1.289 1.298
+ 2ALA HA 10 1.269 1.295 1.401
+ 2ALA CB 11 1.107 1.379 1.286
+ 2ALA HB1 12 1.057 1.360 1.191
+ 2ALA HB2 13 1.034 1.369 1.366
+ 2ALA HB3 14 1.141 1.482 1.282
+ 2ALA C 15 1.192 1.141 1.266
+ 2ALA O 16 1.220 1.089 1.156
+ 3NME N 17 1.131 1.075 1.364
+ 3NME H 18 1.117 1.126 1.450
+ 3NME CH3 19 1.090 0.931 1.376
+ 3NME HH31 20 1.156 0.880 1.446
+ 3NME HH32 21 0.996 0.929 1.431
+ 3NME HH33 22 1.090 0.874 1.283
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 16.00000
+ 22
+ 1ACE HH31 1 1.587 1.386 1.166
+ 1ACE CH3 2 1.554 1.425 1.262
+ 1ACE HH32 3 1.559 1.534 1.266
+ 1ACE HH33 4 1.627 1.390 1.335
+ 1ACE C 5 1.417 1.372 1.300
+ 1ACE O 6 1.390 1.364 1.421
+ 2ALA N 7 1.334 1.344 1.205
+ 2ALA H 8 1.365 1.367 1.111
+ 2ALA CA 9 1.190 1.324 1.235
+ 2ALA HA 10 1.160 1.386 1.319
+ 2ALA CB 11 1.105 1.363 1.112
+ 2ALA HB1 12 1.129 1.297 1.029
+ 2ALA HB2 13 0.999 1.351 1.131
+ 2ALA HB3 14 1.125 1.467 1.088
+ 2ALA C 15 1.162 1.180 1.282
+ 2ALA O 16 1.054 1.128 1.258
+ 3NME N 17 1.261 1.106 1.318
+ 3NME H 18 1.349 1.152 1.336
+ 3NME CH3 19 1.250 0.960 1.324
+ 3NME HH31 20 1.264 0.908 1.229
+ 3NME HH32 21 1.322 0.926 1.399
+ 3NME HH33 22 1.153 0.923 1.357
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 17.00000
+ 22
+ 1ACE HH31 1 1.614 1.382 1.173
+ 1ACE CH3 2 1.559 1.432 1.253
+ 1ACE HH32 3 1.547 1.532 1.213
+ 1ACE HH33 4 1.625 1.444 1.339
+ 1ACE C 5 1.426 1.380 1.288
+ 1ACE O 6 1.411 1.348 1.406
+ 2ALA N 7 1.325 1.370 1.200
+ 2ALA H 8 1.341 1.388 1.102
+ 2ALA CA 9 1.189 1.318 1.239
+ 2ALA HA 10 1.170 1.358 1.338
+ 2ALA CB 11 1.084 1.388 1.158
+ 2ALA HB1 12 1.113 1.369 1.055
+ 2ALA HB2 13 0.994 1.336 1.189
+ 2ALA HB3 14 1.075 1.493 1.186
+ 2ALA C 15 1.170 1.163 1.252
+ 2ALA O 16 1.097 1.103 1.171
+ 3NME N 17 1.235 1.099 1.349
+ 3NME H 18 1.305 1.153 1.399
+ 3NME CH3 19 1.220 0.964 1.393
+ 3NME HH31 20 1.315 0.912 1.406
+ 3NME HH32 21 1.168 0.953 1.489
+ 3NME HH33 22 1.178 0.897 1.318
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 18.00000
+ 22
+ 1ACE HH31 1 1.555 1.419 1.126
+ 1ACE CH3 2 1.554 1.431 1.235
+ 1ACE HH32 3 1.554 1.535 1.267
+ 1ACE HH33 4 1.638 1.381 1.283
+ 1ACE C 5 1.423 1.378 1.292
+ 1ACE O 6 1.416 1.347 1.409
+ 2ALA N 7 1.322 1.351 1.211
+ 2ALA H 8 1.350 1.370 1.115
+ 2ALA CA 9 1.185 1.318 1.251
+ 2ALA HA 10 1.171 1.358 1.352
+ 2ALA CB 11 1.091 1.400 1.149
+ 2ALA HB1 12 1.059 1.346 1.060
+ 2ALA HB2 13 1.008 1.443 1.205
+ 2ALA HB3 14 1.154 1.480 1.109
+ 2ALA C 15 1.163 1.166 1.255
+ 2ALA O 16 1.060 1.108 1.214
+ 3NME N 17 1.255 1.102 1.328
+ 3NME H 18 1.335 1.159 1.354
+ 3NME CH3 19 1.246 0.964 1.369
+ 3NME HH31 20 1.154 0.913 1.344
+ 3NME HH32 21 1.323 0.899 1.327
+ 3NME HH33 22 1.251 0.953 1.477
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 19.00000
+ 22
+ 1ACE HH31 1 1.559 1.326 1.133
+ 1ACE CH3 2 1.552 1.413 1.200
+ 1ACE HH32 3 1.538 1.504 1.142
+ 1ACE HH33 4 1.631 1.428 1.273
+ 1ACE C 5 1.426 1.375 1.280
+ 1ACE O 6 1.428 1.345 1.398
+ 2ALA N 7 1.319 1.363 1.209
+ 2ALA H 8 1.322 1.382 1.110
+ 2ALA CA 9 1.191 1.329 1.265
+ 2ALA HA 10 1.186 1.364 1.368
+ 2ALA CB 11 1.075 1.391 1.178
+ 2ALA HB1 12 1.098 1.383 1.072
+ 2ALA HB2 13 0.980 1.348 1.211
+ 2ALA HB3 14 1.066 1.499 1.192
+ 2ALA C 15 1.169 1.174 1.275
+ 2ALA O 16 1.086 1.118 1.203
+ 3NME N 17 1.233 1.105 1.363
+ 3NME H 18 1.312 1.150 1.405
+ 3NME CH3 19 1.242 0.956 1.350
+ 3NME HH31 20 1.219 0.899 1.440
+ 3NME HH32 21 1.165 0.918 1.284
+ 3NME HH33 22 1.333 0.921 1.301
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 20.00000
+ 22
+ 1ACE HH31 1 1.622 1.459 1.287
+ 1ACE CH3 2 1.546 1.434 1.214
+ 1ACE HH32 3 1.578 1.365 1.135
+ 1ACE HH33 4 1.509 1.531 1.180
+ 1ACE C 5 1.430 1.358 1.283
+ 1ACE O 6 1.444 1.310 1.394
+ 2ALA N 7 1.315 1.370 1.215
+ 2ALA H 8 1.323 1.427 1.132
+ 2ALA CA 9 1.178 1.334 1.258
+ 2ALA HA 10 1.163 1.376 1.357
+ 2ALA CB 11 1.079 1.393 1.158
+ 2ALA HB1 12 1.096 1.348 1.060
+ 2ALA HB2 13 0.979 1.367 1.192
+ 2ALA HB3 14 1.087 1.501 1.165
+ 2ALA C 15 1.163 1.177 1.270
+ 2ALA O 16 1.073 1.114 1.216
+ 3NME N 17 1.249 1.110 1.347
+ 3NME H 18 1.324 1.165 1.388
+ 3NME CH3 19 1.242 0.964 1.360
+ 3NME HH31 20 1.325 0.920 1.416
+ 3NME HH32 21 1.151 0.938 1.414
+ 3NME HH33 22 1.221 0.913 1.266
+ 10.00000 10.00000 10.00000
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/Makefile b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/bias.ves1.iter-10.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/bias.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..55fc4b90e0bb8e0a74059ba4d1ad0bc14e44ef67
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/bias.ves1.iter-10.data.reference
@@ -0,0 +1,105 @@
+#! FIELDS phi ves1.bias der_phi
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET nbins_phi 100
+#! SET periodic_phi true
+ -3.141592654 -1.962887340 -12.338802116
+ -3.078760801 -1.169414064 -12.715200498
+ -3.015928947 -0.391297555 -11.842670932
+ -2.953097094 0.293014687 -9.744489584
+ -2.890265241 0.810780738 -6.578621340
+ -2.827433388 1.103213002 -2.628636251
+ -2.764601535 1.132736781 1.718540218
+ -2.701769682 0.888479952 6.006285748
+ -2.638937829 0.389363553 9.750412598
+ -2.576105976 -0.315622008 12.485919949
+ -2.513274123 -1.150108758 13.813956198
+ -2.450442270 -2.015880754 13.444439030
+ -2.387610417 -2.800832289 11.230078693
+ -2.324778564 -3.388698586 7.188264732
+ -2.261946711 -3.669712459 1.508346390
+ -2.199114858 -3.551225879 -5.456835497
+ -2.136283004 -2.967309202 -13.214845369
+ -2.073451151 -1.886407100 -21.171200499
+ -2.010619298 -0.316284409 -28.677475468
+ -1.947787445 1.694275951 -35.085823711
+ -1.884955592 4.057277381 -39.805102330
+ -1.822123739 6.650758491 -42.353552663
+ -1.759291886 9.327116398 -42.403222481
+ -1.696460033 11.923851076 -39.811998967
+ -1.633628180 14.275849793 -34.640194909
+ -1.570796327 16.228180200 -27.149996573
+ -1.507964474 17.648302059 -17.787615275
+ -1.445132621 18.436646858 -7.149543685
+ -1.382300768 18.534648860 4.064242212
+ -1.319468915 17.929528507 15.106108250
+ -1.256637061 16.655410154 25.240764953
+ -1.193805208 14.790675170 33.804217774
+ -1.130973355 12.451779631 40.256530152
+ -1.068141502 9.784073053 44.223828351
+ -1.005309649 6.950413066 45.525955652
+ -0.942477796 4.118557135 44.187485578
+ -0.879645943 1.448409775 40.431307959
+ -0.816814090 -0.919796122 34.655567695
+ -0.753982237 -2.875401651 27.396218871
+ -0.691150384 -4.344509048 19.278719545
+ -0.628318531 -5.293907399 10.963319829
+ -0.565486678 -5.731488729 3.088904596
+ -0.502654825 -5.703221985 -3.779600964
+ -0.439822972 -5.287056426 -9.195669122
+ -0.376991118 -4.584390419 -12.863688798
+ -0.314159265 -3.709942861 -14.656970625
+ -0.251327412 -2.780984749 -14.620029905
+ -0.188495559 -1.906918090 -12.955414618
+ -0.125663706 -1.180127187 -9.996768596
+ -0.062831853 -0.668881003 -6.171056989
+ 0.000000000 -0.412850137 -1.953818247
+ 0.062831853 -0.421539575 2.178140178
+ 0.125663706 -0.675654705 5.792062628
+ 0.188495559 -1.131140428 8.538354992
+ 0.251327412 -1.725387947 10.179965544
+ 0.314159265 -2.384913757 10.609550868
+ 0.376991118 -3.033697597 9.853189732
+ 0.439822972 -3.601330342 8.060748792
+ 0.502654825 -4.030170819 5.484305244
+ 0.565486678 -4.280835606 2.447166697
+ 0.628318531 -4.335534258 -0.693110509
+ 0.691150384 -4.198993981 -3.583796504
+ 0.753982237 -3.896968936 -5.914139727
+ 0.816814090 -3.472574521 -7.446871847
+ 0.879645943 -2.980902025 -8.041001900
+ 0.942477796 -2.482532833 -7.663790383
+ 1.005309649 -2.036668522 -6.390943538
+ 1.068141502 -1.694615038 -4.395294320
+ 1.130973355 -1.494304801 -1.925415089
+ 1.193805208 -1.456416832 0.723380390
+ 1.256637061 -1.582475512 3.242441860
+ 1.319468915 -1.855092601 5.343983442
+ 1.382300768 -2.240287277 6.792439000
+ 1.445132621 -2.691599109 7.429676026
+ 1.507964474 -3.155521657 7.191454953
+ 1.570796327 -3.577648783 6.113468227
+ 1.633628180 -3.908855525 4.326406440
+ 1.696460033 -4.110837235 2.040661900
+ 1.759291886 -4.160404057 -0.477626840
+ 1.822123739 -4.052064683 -2.936575167
+ 1.884955592 -3.798619184 -5.051347997
+ 1.947787445 -3.429696029 -6.576207401
+ 2.010619298 -2.988390547 -7.332346000
+ 2.073451151 -2.526367898 -7.228480223
+ 2.136283004 -2.097961365 -6.271936183
+ 2.199114858 -1.753908884 -4.568960171
+ 2.261946711 -1.535415076 -2.314123056
+ 2.324778564 -1.469197662 0.230153754
+ 2.387610417 -1.564078476 2.761863469
+ 2.450442270 -1.809520038 4.972532009
+ 2.513274123 -2.176304947 6.581698361
+ 2.576105976 -2.619327928 7.369072046
+ 2.638937829 -3.082242736 7.200869631
+ 2.701769682 -3.503501849 6.047385643
+ 2.764601535 -3.823167726 3.989720592
+ 2.827433388 -3.989777340 1.214684827
+ 2.890265241 -3.966517945 -2.001887206
+ 2.953097094 -3.736025222 -5.321964767
+ 3.015928947 -3.303241013 -8.379756402
+ 3.078760801 -2.695955240 -10.820370974
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/coeffs.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/coeffs.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..478cffec045c1a8bfd01d84cb123d22f99f8168b
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/coeffs.data.reference
@@ -0,0 +1,231 @@
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.000000 0.000000 1
+ 2 0.000000 0.000000 2
+ 3 0.000000 0.000000 3
+ 4 0.000000 0.000000 4
+ 5 0.000000 0.000000 5
+ 6 0.000000 0.000000 6
+ 7 0.000000 0.000000 7
+ 8 0.000000 0.000000 8
+ 9 0.000000 0.000000 9
+ 10 0.000000 0.000000 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.219197 0.219197 1
+ 2 -0.970366 -0.970366 2
+ 3 -0.884094 -0.884094 3
+ 4 -0.421298 -0.421298 4
+ 5 -0.590820 -0.590820 5
+ 6 0.748809 0.748809 6
+ 7 0.576392 0.576392 7
+ 8 0.715341 0.715341 8
+ 9 0.786645 0.786645 9
+ 10 -0.381816 -0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.305152 0.391107 1
+ 2 -1.461895 -1.953423 2
+ 3 -1.350614 -1.817134 3
+ 4 -0.589608 -0.757918 4
+ 5 -0.834473 -1.078125 5
+ 6 1.174985 1.601160 6
+ 7 0.948813 1.321234 7
+ 8 1.024273 1.333206 8
+ 9 1.148264 1.509884 9
+ 10 -0.689625 -0.997434 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.421218 0.653351 1
+ 2 -1.946133 -2.914610 2
+ 3 -1.788707 -2.664892 3
+ 4 -0.812257 -1.257555 4
+ 5 -1.146186 -1.769612 5
+ 6 1.540202 2.270638 6
+ 7 1.220946 1.765213 7
+ 8 1.401662 2.156440 8
+ 9 1.564119 2.395830 9
+ 10 -0.857540 -1.193370 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.448007 0.528372 1
+ 2 -2.433590 -3.895961 2
+ 3 -2.239120 -3.590362 3
+ 4 -0.861012 -1.007276 4
+ 5 -1.209573 -1.399733 5
+ 6 1.931358 3.104824 6
+ 7 1.535645 2.479741 7
+ 8 1.472935 1.686754 8
+ 9 1.639154 1.864258 9
+ 10 -1.086629 -1.773897 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.441146 0.413704 1
+ 2 -2.895058 -4.740930 2
+ 3 -2.593087 -4.008954 3
+ 4 -0.858951 -0.850710 4
+ 5 -1.239599 -1.359702 5
+ 6 2.140456 2.976852 6
+ 7 1.611231 1.913575 7
+ 8 1.562246 1.919487 8
+ 9 1.789475 2.390761 9
+ 10 -1.071904 -1.013004 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.441948 0.445955 1
+ 2 -3.365271 -5.716337 2
+ 3 -2.979506 -4.911603 3
+ 4 -0.867479 -0.910117 4
+ 5 -1.269466 -1.418805 5
+ 6 2.410784 3.762420 6
+ 7 1.766861 2.545012 7
+ 8 1.621663 1.918750 8
+ 9 1.870932 2.278215 9
+ 10 -1.136982 -1.462370 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.383175 0.030542 1
+ 2 -3.758763 -6.119715 2
+ 3 -3.154779 -4.206413 3
+ 4 -0.874583 -0.917208 4
+ 5 -1.387569 -2.096189 5
+ 6 2.602191 3.750634 6
+ 7 1.994254 3.358610 7
+ 8 1.747113 2.499816 8
+ 9 1.915919 2.185842 9
+ 10 -1.282146 -2.153134 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.296543 -0.309884 1
+ 2 -4.141493 -6.820603 2
+ 3 -3.290550 -4.240951 3
+ 4 -0.837652 -0.579136 4
+ 5 -1.491646 -2.220179 5
+ 6 2.688068 3.289207 6
+ 7 2.149365 3.235145 7
+ 8 1.917967 3.113944 8
+ 9 2.038602 2.897379 9
+ 10 -1.468354 -2.771810 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.234442 -0.262361 1
+ 2 -4.548948 -7.808582 2
+ 3 -3.501952 -5.193167 3
+ 4 -0.818965 -0.669467 4
+ 5 -1.579418 -2.281596 5
+ 6 2.854156 4.182861 6
+ 7 2.360190 4.046783 7
+ 8 2.050168 3.107779 8
+ 9 2.134519 2.901856 9
+ 10 -1.691816 -3.479514 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.coeffs ves1.aux_coeffs index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0.000000 0
+ 1 0.205729 -0.052695 1
+ 2 -4.971305 -8.772526 2
+ 3 -3.756567 -6.048102 3
+ 4 -0.842988 -1.059199 4
+ 5 -1.697444 -2.759682 5
+ 6 3.054607 4.858669 6
+ 7 2.568698 4.445279 7
+ 8 2.208072 3.629202 8
+ 9 2.266734 3.456672 9
+ 10 -1.877002 -3.543669 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/colvar.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/colvar.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d1d516bcc2d66523125a380459cf3cee3988f789
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/colvar.data.reference
@@ -0,0 +1,24 @@
+#! FIELDS time phi ves1.bias o1.gradrms o1.gradmax
+#! SET min_phi -pi
+#! SET max_phi pi
+ 0.000000 -1.238 0.000 0.000 0.000
+ 1.000000 -1.484 0.000 0.000 0.000
+ 2.000000 -1.324 0.000 0.637 0.970
+ 3.000000 -1.334 4.716 0.637 0.970
+ 4.000000 -1.461 4.403 0.659 0.983
+ 5.000000 -1.220 6.371 0.659 0.983
+ 6.000000 -1.388 7.123 0.649 0.961
+ 7.000000 -1.548 7.766 0.649 0.961
+ 8.000000 -1.843 1.066 0.599 0.981
+ 9.000000 -2.242 -3.365 0.599 0.981
+ 10.000000 -1.148 8.387 0.439 0.847
+ 11.000000 -1.758 5.325 0.439 0.847
+ 12.000000 -1.319 12.218 0.523 0.975
+ 13.000000 -2.991 -1.159 0.523 0.975
+ 14.000000 -1.411 13.737 0.475 0.814
+ 15.000000 -2.599 -0.714 0.475 0.814
+ 16.000000 -1.461 14.602 0.451 0.755
+ 17.000000 -1.379 15.945 0.451 0.755
+ 18.000000 -1.677 10.610 0.598 0.988
+ 19.000000 -1.524 16.005 0.598 0.988
+ 20.000000 -1.200 13.955 0.585 0.965
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/combined_gradient.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/combined_gradient.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..fd2741b6458ded2a3525e6ef0197241c4d2b8000
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/combined_gradient.data.reference
@@ -0,0 +1,210 @@
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 2.000000
+#! SET iteration 1
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.219197 1
+ 2 0.970366 2
+ 3 0.884094 3
+ 4 0.421298 4
+ 5 0.590820 5
+ 6 -0.748809 6
+ 7 -0.576392 7
+ 8 -0.715341 8
+ 9 -0.786645 9
+ 10 0.381816 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 4.000000
+#! SET iteration 2
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.171909 1
+ 2 0.983056 2
+ 3 0.933040 3
+ 4 0.336620 4
+ 5 0.487305 5
+ 6 -0.852350 6
+ 7 -0.744842 7
+ 8 -0.617866 8
+ 9 -0.723239 9
+ 10 0.615618 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 6.000000
+#! SET iteration 3
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.262244 1
+ 2 0.961187 2
+ 3 0.847758 3
+ 4 0.499637 4
+ 5 0.691487 5
+ 6 -0.669478 6
+ 7 -0.443979 7
+ 8 -0.823233 8
+ 9 -0.885946 9
+ 10 0.195936 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 8.000000
+#! SET iteration 4
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.124979 1
+ 2 0.981351 2
+ 3 0.925470 3
+ 4 -0.250280 4
+ 5 -0.369879 5
+ 6 -0.834186 6
+ 7 -0.714529 7
+ 8 0.469686 8
+ 9 0.531572 9
+ 10 0.580527 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 10.000000
+#! SET iteration 5
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.114667 1
+ 2 0.844969 2
+ 3 0.418592 3
+ 4 -0.156566 4
+ 5 -0.040031 5
+ 6 0.127972 6
+ 7 0.566166 7
+ 8 -0.232733 8
+ 9 -0.526503 9
+ 10 -0.760892 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 12.000000
+#! SET iteration 6
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.032251 1
+ 2 0.975407 2
+ 3 0.902649 3
+ 4 0.059408 4
+ 5 0.059102 5
+ 6 -0.785568 6
+ 7 -0.631437 7
+ 8 0.000738 8
+ 9 0.112546 9
+ 10 0.449365 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 14.000000
+#! SET iteration 7
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.415413 1
+ 2 0.403378 2
+ 3 -0.705190 3
+ 4 0.007091 4
+ 5 0.677384 5
+ 6 0.011786 6
+ 7 -0.813598 7
+ 8 -0.581066 8
+ 9 0.092373 9
+ 10 0.690764 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 16.000000
+#! SET iteration 8
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 0.340425 1
+ 2 0.700888 2
+ 3 0.034538 3
+ 4 -0.338072 4
+ 5 0.123991 5
+ 6 0.461427 6
+ 7 0.123465 7
+ 8 -0.614128 8
+ 9 -0.711537 9
+ 10 0.618677 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 18.000000
+#! SET iteration 9
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.047522 1
+ 2 0.987979 2
+ 3 0.952216 3
+ 4 0.090331 4
+ 5 0.061417 5
+ 6 -0.893654 6
+ 7 -0.811638 7
+ 8 0.006164 8
+ 9 -0.004477 9
+ 10 0.707703 10
+#!-------------------
+
+
+#! FIELDS idx_phi ves1.combined_gradient index
+#! SET time 20.000000
+#! SET iteration 10
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 0.000000 0
+ 1 -0.209666 1
+ 2 0.963944 2
+ 3 0.854935 3
+ 4 0.389732 4
+ 5 0.478086 5
+ 6 -0.675807 6
+ 7 -0.398496 7
+ 8 -0.521422 8
+ 9 -0.554816 9
+ 10 0.064155 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/config b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/config
new file mode 100644
index 0000000000000000000000000000000000000000..d9b022c5f95c12fdf3de7e32807e196863eec343
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/config
@@ -0,0 +1,3 @@
+plumed_modules=ves
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro --dump-forces forces --dump-forces-fmt=%10.6f "
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/fes.ves1.iter-10.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/fes.ves1.iter-10.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..d50483ac34516d62eac2c7fd2592ae5ef72ba0af
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/fes.ves1.iter-10.data.reference
@@ -0,0 +1,105 @@
+#! FIELDS phi ves1.fes
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET nbins_phi 100
+#! SET periodic_phi true
+ -3.141592654 20.497536200
+ -3.078760801 19.704062923
+ -3.015928947 18.925946415
+ -2.953097094 18.241634172
+ -2.890265241 17.723868121
+ -2.827433388 17.431435858
+ -2.764601535 17.401912078
+ -2.701769682 17.646168907
+ -2.638937829 18.145285307
+ -2.576105976 18.850270868
+ -2.513274123 19.684757617
+ -2.450442270 20.550529614
+ -2.387610417 21.335481149
+ -2.324778564 21.923347445
+ -2.261946711 22.204361318
+ -2.199114858 22.085874739
+ -2.136283004 21.501958062
+ -2.073451151 20.421055959
+ -2.010619298 18.850933268
+ -1.947787445 16.840372909
+ -1.884955592 14.477371479
+ -1.822123739 11.883890368
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diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/forces.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/forces.reference
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index 0000000000000000000000000000000000000000..75ae219e0f6736a9037c0c36631fa4ee84749782
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diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/plumed.dat b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/plumed.dat
new file mode 100644
index 0000000000000000000000000000000000000000..dc1819aeededff7bccd844a2538ba4d9dd273ef6
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/plumed.dat
@@ -0,0 +1,43 @@
+# vim:ft=plumed
+
+phi: TORSION ATOMS=5,7,9,15 NOPBC
+
+bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi
+
+VES_LINEAR_EXPANSION ...
+ ARG=phi
+ BASIS_FUNCTIONS=bf1
+ LABEL=ves1
+ TEMP=300.0
+ GRID_BINS=100
+... VES_LINEAR_EXPANSION
+
+# NOTE: These parameters do not reflect parameters used in real simulations!
+# This is only for testing!
+#
+
+OPT_AVERAGED_SGD ...
+ BIAS=ves1
+ STRIDE=1000
+ LABEL=o1
+ STEPSIZE=1.0
+ COEFFS_FILE=coeffs.data
+ COEFFS_OUTPUT=1
+ COEFFS_FMT=%12.6f
+ FES_OUTPUT=10
+ BIAS_OUTPUT=10
+ TARGETDIST_AVERAGES_FMT=%12.6f
+ COMBINED_GRADIENT_FILE=combined_gradient.data
+ COMBINED_GRADIENT_OUTPUT=1
+ COMBINED_GRADIENT_FMT=%12.6f
+ MONITOR_INSTANTANEOUS_GRADIENT
+... OPT_AVERAGED_SGD
+
+PRINT ...
+ STRIDE=500
+ ARG=phi,ves1.bias,o1.*
+ FILE=colvar.data FMT=%6.3f
+... PRINT
+
+ENDPLUMED
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/targetdist-averages.data.reference b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/targetdist-averages.data.reference
new file mode 100644
index 0000000000000000000000000000000000000000..b6bf5b55ccca602f2814808f51085a0599e101ab
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/targetdist-averages.data.reference
@@ -0,0 +1,21 @@
+#! FIELDS idx_phi ves1.targetdist_averages index
+#! SET time 0.000000
+#! SET iteration 0
+#! SET type LinearBasisSet
+#! SET ndimensions 1
+#! SET ncoeffs_total 11
+#! SET shape_phi 11
+ 0 1.000000 0
+ 1 0.000000 1
+ 2 0.000000 2
+ 3 0.000000 3
+ 4 0.000000 4
+ 5 0.000000 5
+ 6 0.000000 6
+ 7 0.000000 7
+ 8 0.000000 8
+ 9 0.000000 9
+ 10 0.000000 10
+#!-------------------
+
+
diff --git a/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/traj.gro b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/traj.gro
new file mode 100644
index 0000000000000000000000000000000000000000..c1c387a0144ec8021b9e5b0453be534f2ca906e2
--- /dev/null
+++ b/regtest/ves/rt-opt-averaged-sgd-monitor-inst-grad/traj.gro
@@ -0,0 +1,525 @@
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 0.00000
+ 22
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+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 1.00000
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+ 3NME HH32 21 1.233 0.990 1.511
+ 3NME HH33 22 1.241 1.141 1.596
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 2.00000
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 3.00000
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 4.00000
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 5.00000
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+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 6.00000
+ 22
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 7.00000
+ 22
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+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 8.00000
+ 22
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+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 9.00000
+ 22
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 10.00000
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 11.00000
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 12.00000
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+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 13.00000
+ 22
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+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 14.00000
+ 22
+ 1ACE HH31 1 1.543 1.468 1.123
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+ 3NME HH32 21 1.293 0.868 1.270
+ 3NME HH33 22 1.292 0.934 1.434
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 15.00000
+ 22
+ 1ACE HH31 1 1.508 1.417 1.043
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+ 2ALA HA 10 1.269 1.295 1.401
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+ 2ALA HB1 12 1.057 1.360 1.191
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+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 16.00000
+ 22
+ 1ACE HH31 1 1.587 1.386 1.166
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+ 2ALA CB 11 1.105 1.363 1.112
+ 2ALA HB1 12 1.129 1.297 1.029
+ 2ALA HB2 13 0.999 1.351 1.131
+ 2ALA HB3 14 1.125 1.467 1.088
+ 2ALA C 15 1.162 1.180 1.282
+ 2ALA O 16 1.054 1.128 1.258
+ 3NME N 17 1.261 1.106 1.318
+ 3NME H 18 1.349 1.152 1.336
+ 3NME CH3 19 1.250 0.960 1.324
+ 3NME HH31 20 1.264 0.908 1.229
+ 3NME HH32 21 1.322 0.926 1.399
+ 3NME HH33 22 1.153 0.923 1.357
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 17.00000
+ 22
+ 1ACE HH31 1 1.614 1.382 1.173
+ 1ACE CH3 2 1.559 1.432 1.253
+ 1ACE HH32 3 1.547 1.532 1.213
+ 1ACE HH33 4 1.625 1.444 1.339
+ 1ACE C 5 1.426 1.380 1.288
+ 1ACE O 6 1.411 1.348 1.406
+ 2ALA N 7 1.325 1.370 1.200
+ 2ALA H 8 1.341 1.388 1.102
+ 2ALA CA 9 1.189 1.318 1.239
+ 2ALA HA 10 1.170 1.358 1.338
+ 2ALA CB 11 1.084 1.388 1.158
+ 2ALA HB1 12 1.113 1.369 1.055
+ 2ALA HB2 13 0.994 1.336 1.189
+ 2ALA HB3 14 1.075 1.493 1.186
+ 2ALA C 15 1.170 1.163 1.252
+ 2ALA O 16 1.097 1.103 1.171
+ 3NME N 17 1.235 1.099 1.349
+ 3NME H 18 1.305 1.153 1.399
+ 3NME CH3 19 1.220 0.964 1.393
+ 3NME HH31 20 1.315 0.912 1.406
+ 3NME HH32 21 1.168 0.953 1.489
+ 3NME HH33 22 1.178 0.897 1.318
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 18.00000
+ 22
+ 1ACE HH31 1 1.555 1.419 1.126
+ 1ACE CH3 2 1.554 1.431 1.235
+ 1ACE HH32 3 1.554 1.535 1.267
+ 1ACE HH33 4 1.638 1.381 1.283
+ 1ACE C 5 1.423 1.378 1.292
+ 1ACE O 6 1.416 1.347 1.409
+ 2ALA N 7 1.322 1.351 1.211
+ 2ALA H 8 1.350 1.370 1.115
+ 2ALA CA 9 1.185 1.318 1.251
+ 2ALA HA 10 1.171 1.358 1.352
+ 2ALA CB 11 1.091 1.400 1.149
+ 2ALA HB1 12 1.059 1.346 1.060
+ 2ALA HB2 13 1.008 1.443 1.205
+ 2ALA HB3 14 1.154 1.480 1.109
+ 2ALA C 15 1.163 1.166 1.255
+ 2ALA O 16 1.060 1.108 1.214
+ 3NME N 17 1.255 1.102 1.328
+ 3NME H 18 1.335 1.159 1.354
+ 3NME CH3 19 1.246 0.964 1.369
+ 3NME HH31 20 1.154 0.913 1.344
+ 3NME HH32 21 1.323 0.899 1.327
+ 3NME HH33 22 1.251 0.953 1.477
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 19.00000
+ 22
+ 1ACE HH31 1 1.559 1.326 1.133
+ 1ACE CH3 2 1.552 1.413 1.200
+ 1ACE HH32 3 1.538 1.504 1.142
+ 1ACE HH33 4 1.631 1.428 1.273
+ 1ACE C 5 1.426 1.375 1.280
+ 1ACE O 6 1.428 1.345 1.398
+ 2ALA N 7 1.319 1.363 1.209
+ 2ALA H 8 1.322 1.382 1.110
+ 2ALA CA 9 1.191 1.329 1.265
+ 2ALA HA 10 1.186 1.364 1.368
+ 2ALA CB 11 1.075 1.391 1.178
+ 2ALA HB1 12 1.098 1.383 1.072
+ 2ALA HB2 13 0.980 1.348 1.211
+ 2ALA HB3 14 1.066 1.499 1.192
+ 2ALA C 15 1.169 1.174 1.275
+ 2ALA O 16 1.086 1.118 1.203
+ 3NME N 17 1.233 1.105 1.363
+ 3NME H 18 1.312 1.150 1.405
+ 3NME CH3 19 1.242 0.956 1.350
+ 3NME HH31 20 1.219 0.899 1.440
+ 3NME HH32 21 1.165 0.918 1.284
+ 3NME HH33 22 1.333 0.921 1.301
+ 10.00000 10.00000 10.00000
+Generated by trjconv : Gromacs Runs One Microsecond At Cannonball Speeds t= 20.00000
+ 22
+ 1ACE HH31 1 1.622 1.459 1.287
+ 1ACE CH3 2 1.546 1.434 1.214
+ 1ACE HH32 3 1.578 1.365 1.135
+ 1ACE HH33 4 1.509 1.531 1.180
+ 1ACE C 5 1.430 1.358 1.283
+ 1ACE O 6 1.444 1.310 1.394
+ 2ALA N 7 1.315 1.370 1.215
+ 2ALA H 8 1.323 1.427 1.132
+ 2ALA CA 9 1.178 1.334 1.258
+ 2ALA HA 10 1.163 1.376 1.357
+ 2ALA CB 11 1.079 1.393 1.158
+ 2ALA HB1 12 1.096 1.348 1.060
+ 2ALA HB2 13 0.979 1.367 1.192
+ 2ALA HB3 14 1.087 1.501 1.165
+ 2ALA C 15 1.163 1.177 1.270
+ 2ALA O 16 1.073 1.114 1.216
+ 3NME N 17 1.249 1.110 1.347
+ 3NME H 18 1.324 1.165 1.388
+ 3NME CH3 19 1.242 0.964 1.360
+ 3NME HH31 20 1.325 0.920 1.416
+ 3NME HH32 21 1.151 0.938 1.414
+ 3NME HH33 22 1.221 0.913 1.266
+ 10.00000 10.00000 10.00000
diff --git a/regtest/ves/rt-opt-averaged-sgd/colvar.data.reference b/regtest/ves/rt-opt-averaged-sgd/colvar.data.reference
index d1d516bcc2d66523125a380459cf3cee3988f789..7aeeeabc0fecc81e64d9f6e774cc10fdf403636e 100644
--- a/regtest/ves/rt-opt-averaged-sgd/colvar.data.reference
+++ b/regtest/ves/rt-opt-averaged-sgd/colvar.data.reference
@@ -1,24 +1,24 @@
-#! FIELDS time phi ves1.bias o1.gradrms o1.gradmax
+#! FIELDS time phi ves1.bias
#! SET min_phi -pi
#! SET max_phi pi
- 0.000000 -1.238 0.000 0.000 0.000
- 1.000000 -1.484 0.000 0.000 0.000
- 2.000000 -1.324 0.000 0.637 0.970
- 3.000000 -1.334 4.716 0.637 0.970
- 4.000000 -1.461 4.403 0.659 0.983
- 5.000000 -1.220 6.371 0.659 0.983
- 6.000000 -1.388 7.123 0.649 0.961
- 7.000000 -1.548 7.766 0.649 0.961
- 8.000000 -1.843 1.066 0.599 0.981
- 9.000000 -2.242 -3.365 0.599 0.981
- 10.000000 -1.148 8.387 0.439 0.847
- 11.000000 -1.758 5.325 0.439 0.847
- 12.000000 -1.319 12.218 0.523 0.975
- 13.000000 -2.991 -1.159 0.523 0.975
- 14.000000 -1.411 13.737 0.475 0.814
- 15.000000 -2.599 -0.714 0.475 0.814
- 16.000000 -1.461 14.602 0.451 0.755
- 17.000000 -1.379 15.945 0.451 0.755
- 18.000000 -1.677 10.610 0.598 0.988
- 19.000000 -1.524 16.005 0.598 0.988
- 20.000000 -1.200 13.955 0.585 0.965
+ 0.000000 -1.238 0.000
+ 1.000000 -1.484 0.000
+ 2.000000 -1.324 0.000
+ 3.000000 -1.334 4.716
+ 4.000000 -1.461 4.403
+ 5.000000 -1.220 6.371
+ 6.000000 -1.388 7.123
+ 7.000000 -1.548 7.766
+ 8.000000 -1.843 1.066
+ 9.000000 -2.242 -3.365
+ 10.000000 -1.148 8.387
+ 11.000000 -1.758 5.325
+ 12.000000 -1.319 12.218
+ 13.000000 -2.991 -1.159
+ 14.000000 -1.411 13.737
+ 15.000000 -2.599 -0.714
+ 16.000000 -1.461 14.602
+ 17.000000 -1.379 15.945
+ 18.000000 -1.677 10.610
+ 19.000000 -1.524 16.005
+ 20.000000 -1.200 13.955
diff --git a/regtest/ves/rt-opt-averaged-sgd/plumed.dat b/regtest/ves/rt-opt-averaged-sgd/plumed.dat
index b5b82727dc88eca3718dff39356f610b27709f1d..339ced334ccdee58a9d2548a57f321bb1dcd6f9d 100644
--- a/regtest/ves/rt-opt-averaged-sgd/plumed.dat
+++ b/regtest/ves/rt-opt-averaged-sgd/plumed.dat
@@ -34,7 +34,7 @@ OPT_AVERAGED_SGD ...
PRINT ...
STRIDE=500
- ARG=phi,ves1.bias,o1.*
+ ARG=phi,ves1.bias
FILE=colvar.data FMT=%6.3f
... PRINT
diff --git a/regtest/ves/rt-opt-dummy/plumed.dat b/regtest/ves/rt-opt-dummy/plumed.dat
index a07e8d63167ada378107fc6208e443e39837647d..38b7cc0c2157bdd1719da3dc9a54539f1c1bff92 100644
--- a/regtest/ves/rt-opt-dummy/plumed.dat
+++ b/regtest/ves/rt-opt-dummy/plumed.dat
@@ -33,6 +33,7 @@ OPT_DUMMY ...
HESSIAN_OUTPUT=1
HESSIAN_FMT=%12.6f
TARGETDIST_AVERAGES_FMT=%12.6f
+ MONITOR_INSTANTANEOUS_GRADIENT
... OPT_DUMMY
PRINT ...
diff --git a/scripts/partial_tempering.sh b/scripts/partial_tempering.sh
index e3dc15dcf901857a659e7de7bb3d41465c80ef59..2e5f1832bac6276ef3c72e19c21ef3a0afd649ba 100755
--- a/scripts/partial_tempering.sh
+++ b/scripts/partial_tempering.sh
@@ -1,3 +1,4 @@
+# vim:ft=awk
if [ "$1" = --description ] ; then
echo "create a new collective variable from a template"
exit 0
@@ -7,7 +8,7 @@ if [ "$1" = --help ] || [ "$1" = -h ] ; then
cat <<EOF
Usage:
- plumed partial_tempering scale < processed.top
+ plumed partial_tempering [--gromacs4] scale < processed.top
where scale is the Hamiltonian scaling factor and
processed.top is a post-processed topology file (i.e. produced with grompp -pp)
@@ -55,7 +56,14 @@ EOF
exit
fi
-awk -v scale=$1 '
+gromacs5=1
+
+if [ $1 == --gromacs4 ] ; then
+ gromacs5=0
+ shift
+fi
+
+awk -v scale=$1 -v gromacs5=$gromacs5 '
BEGIN{
combrule=1;
}
@@ -73,6 +81,39 @@ function warning(msg)
{
print "WARNING:",msg | "cat 1>&2"
}
+function find_matching_torsion(params,atype, a1,a2,a3,a4,iswitch,progression,test,array,param,countX,bestCountX,bestMatch)
+{
+ progression=NR
+ bestCountX=5
+ for(iswitch=0;iswitch<32;iswitch++){
+ countX=0
+ if(iswitch%2==0){
+ a1=atype[1]; a2=atype[2]; a3=atype[3]; a4=atype[4];
+ } else {
+ a1=atype[4]; a2=atype[3]; a3=atype[2]; a4=atype[1];
+ }
+ if(int(iswitch/2)%2==1){ a1="X"; countX++; }
+ if(int(iswitch/4)%2==1){ a2="X"; countX++; }
+ if(int(iswitch/8)%2==1){ a3="X"; countX++; }
+ if(int(iswitch/16)%2==1){a4="X"; countX++; }
+ test=a1"-"a2"-"a3"-"a4"-"$5;
+ if(test in params){
+ split(params[test],array,":");
+ bestMatch=0;
+ if(gromacs5) {
+ if(countX<bestCountX || (countX==bestCountX && array[1]<progression)) bestMatch=1
+ } else {
+ if(array[1]<progression) bestMatch=1;
+ }
+ if(bestMatch){
+ progression=array[1];
+ bestCountX=countX
+ param=params[test];
+ }
+ }
+ }
+ return param;
+}
{
# This is the suffix for "hot" atoms:
suffix="_";
@@ -185,27 +226,9 @@ function warning(msg)
atype[2]=bondtype[ato[$2]]
atype[3]=bondtype[ato[$3]]
atype[4]=bondtype[ato[$4]]
+
+ param=find_matching_torsion(params,atype);
- progression=NR
- for(iswitch=0;iswitch<32;iswitch++){
- if(iswitch%2==0){
- a1=atype[1]; a2=atype[2]; a3=atype[3]; a4=atype[4];
- } else {
- a1=atype[4]; a2=atype[3]; a3=atype[2]; a4=atype[1];
- }
- if(int(iswitch/2)%2==1) a1="X";
- if(int(iswitch/4)%2==1) a2="X";
- if(int(iswitch/8)%2==1) a3="X";
- if(int(iswitch/16)%2==1) a4="X";
- test=a1"-"a2"-"a3"-"a4"-"$5;
- if(test in params){
- split(params[test],array,":");
- if(array[1]<progression){
- progression=array[1];
- param=params[test];
- }
- }
- }
n=split(param,array,":");
if(n<=1) error("params not found "$1" "$2" "$3" "$4" "$5" "atype[1]" "atype[2]" "atype[3]" "atype[4]);
diff --git a/src/adjmat/ContactMatrix.cpp b/src/adjmat/ContactMatrix.cpp
index 9b945c602f694cca7836b379a1ee642610634535..6622c2826fbcf37a3fe946fbfdabbd183e2e4671 100644
--- a/src/adjmat/ContactMatrix.cpp
+++ b/src/adjmat/ContactMatrix.cpp
@@ -135,11 +135,10 @@ double ContactMatrix::calculateWeight( const unsigned& taskCode, const double& w
double ContactMatrix::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
- double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).calculate( distance.modulo(), dfunc );
+ double dfunc;
+ double sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).calculate( distance.modulo(), dfunc );
if( !doNotCalculateDerivatives() ) {
- Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
- double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).calculate( distance.modulo(), dfunc );
addAtomDerivatives( 1, 0, (-dfunc)*distance, myatoms );
addAtomDerivatives( 1, 1, (+dfunc)*distance, myatoms );
myatoms.addBoxDerivatives( 1, (-dfunc)*Tensor(distance,distance) );
diff --git a/src/adjmat/Sprint.cpp b/src/adjmat/Sprint.cpp
index 8a4c1fe58bc9018b77db93fd5e7f392e38743f3c..04a10bd6ee794321fa0303d3bd72a98d79dead96 100644
--- a/src/adjmat/Sprint.cpp
+++ b/src/adjmat/Sprint.cpp
@@ -173,7 +173,7 @@ void Sprint::calculate() {
startnum += nthis;
}
// Set the sprint coordinates
- for(unsigned icomp=0; icomp<getNumberOfComponents(); ++icomp) {
+ for(int icomp=0; icomp<getNumberOfComponents(); ++icomp) {
getPntrToComponent(icomp)->set( sqrtn*lambda*maxeig[icomp].first );
}
@@ -190,7 +190,7 @@ void Sprint::calculate() {
for(unsigned i=rank; i<active_elements.getNumberActive(); i+=stride) {
unsigned j, k; getAdjacencyVessel()->getMatrixIndices( active_elements[i], j, k );
double tmp1 = 2 * eigenvecs(nval-1,j)*eigenvecs(nval-1,k);
- for(unsigned icomp=0; icomp<getNumberOfComponents(); ++icomp) {
+ for(int icomp=0; icomp<getNumberOfComponents(); ++icomp) {
double tmp2 = 0.;
for(unsigned n=0; n<nval-1; ++n) { // Need care on following line
tmp2 += eigenvecs(n,maxeig[icomp].second) * ( eigenvecs(n,j)*eigenvecs(nval-1,k) + eigenvecs(n,k)*eigenvecs(nval-1,j) ) / ( lambda - eigvals[n] );
@@ -205,7 +205,7 @@ void Sprint::calculate() {
}
if( !serialCalculation() ) comm.Sum( mymat_ders );
- for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+ for(int j=0; j<getNumberOfComponents(); ++j) {
Value* val=getPntrToComponent(j);
for(unsigned i=0; i<getNumberOfDerivatives(); ++i) val->addDerivative( i, mymat_ders(j,i) );
}
@@ -217,7 +217,7 @@ void Sprint::apply() {
unsigned nat=getNumberOfAtoms();
std::vector<double> forces( 3*getNumberOfAtoms() + 9 );
- for(unsigned i=0; i<getNumberOfComponents(); ++i) {
+ for(int i=0; i<getNumberOfComponents(); ++i) {
if( getPntrToComponent(i)->applyForce( forces ) ) {
for(unsigned j=0; j<nat; ++j) {
f[j][0]+=forces[3*j+0];
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 0654a325517ae1a647173dd5f2b73ff9922b4fda..5587c173f20b7027f1fb780b4fbb830503f3b3b4 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -401,7 +401,7 @@ void Histogram::prepareForAveraging() {
std::vector<double> point( getNumberOfArguments() );
for(unsigned i=0; i<point.size(); ++i) point[i]=getArgument(i);
unsigned num_neigh; std::vector<unsigned> neighbors(1);
- kernel.reset(myhist->getKernelAndNeighbors( point, num_neigh, neighbors ));
+ kernel=myhist->getKernelAndNeighbors( point, num_neigh, neighbors );
if( num_neigh>1 ) {
// Activate relevant tasks
@@ -442,7 +442,7 @@ void Histogram::compute( const unsigned& current, MultiValue& myvals ) const {
} else if( myvessels.size()>0 ) {
std::vector<double> cvals( myvessels[0]->getNumberOfQuantities() );
stashes[0]->retrieveSequentialValue( current, false, cvals );
- unsigned derbase; double totweight=cvals[0], tnorm = cvals[0]; myvals.setValue( 1, cvals[1] );
+ unsigned derbase=0; double totweight=cvals[0], tnorm = cvals[0]; myvals.setValue( 1, cvals[1] );
// Get the derivatives as well if we are in apply
if( in_apply ) {
// This bit gets the total weight
diff --git a/src/analysis/PCA.cpp b/src/analysis/PCA.cpp
index feed969e1dbdda3c1177c711bc560883debf71c6..b2b78982bf195615c9ceb7f85cb84e355d1e2041 100644
--- a/src/analysis/PCA.cpp
+++ b/src/analysis/PCA.cpp
@@ -159,7 +159,7 @@ void PCA::performAnalysis() {
// Calculate the average displacement from the first frame
double norm=getWeight(0);
for(unsigned i=1; i<getNumberOfDataPoints(); ++i) {
- double d = data[0]->calc( data[i]->getReferencePositions(), getPbc(), getArguments(), data[i]->getReferenceArguments(), mypack, true );
+ data[0]->calc( data[i]->getReferencePositions(), getPbc(), getArguments(), data[i]->getReferenceArguments(), mypack, true );
// Accumulate average displacement of arguments (Here PBC could do fucked up things - really needs Berry Phase ) GAT
for(unsigned j=0; j<getNumberOfArguments(); ++j) sarg[j] += 0.5*getWeight(i)*mypack.getArgumentDerivative(j);
// Accumulate average displacement of position
@@ -178,7 +178,7 @@ void PCA::performAnalysis() {
Matrix<double> covar( getNumberOfArguments()+3*getNumberOfAtoms(), getNumberOfArguments()+3*getNumberOfAtoms() ); covar=0;
for(unsigned i=0; i<getNumberOfDataPoints(); ++i) {
// double d = data[i]->calc( spos, getPbc(), getArguments(), sarg, mypack, true );
- double d = data[0]->calc( data[i]->getReferencePositions(), getPbc(), getArguments(), data[i]->getReferenceArguments(), mypack, true );
+ data[0]->calc( data[i]->getReferencePositions(), getPbc(), getArguments(), data[i]->getReferenceArguments(), mypack, true );
for(unsigned jarg=0; jarg<getNumberOfArguments(); ++jarg) {
// Need sorting for PBC with GAT
double jarg_d = 0.5*mypack.getArgumentDerivative(jarg) + data[0]->getReferenceArguments()[jarg] - sarg[jarg];
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 56a998710781399d9fda92a73059c638962aab65..0dbbd4994ce4bb87d490a0a31c84aa8aec90bb17 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -98,6 +98,7 @@ class External : public Bias {
private:
std::unique_ptr<Grid> BiasGrid_;
+ double scale_;
public:
explicit External(const ActionOptions&);
@@ -113,6 +114,7 @@ void External::registerKeywords(Keywords& keys) {
keys.add("compulsory","FILE","the name of the file containing the external potential.");
keys.addFlag("NOSPLINE",false,"specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential");
keys.addFlag("SPARSE",false,"specifies that the external potential uses a sparse grid");
+ keys.add("compulsory","SCALE","1.0","a factor that multiplies the external potential, usefull to invert free energies");
}
External::External(const ActionOptions& ao):
@@ -126,10 +128,12 @@ External::External(const ActionOptions& ao):
bool nospline=false;
parseFlag("NOSPLINE",nospline);
bool spline=!nospline;
+ parse("SCALE",scale_);
checkRead();
log.printf(" External potential from file %s\n",filename.c_str());
+ log.printf(" Multiplied by %lf\n",scale_);
if(spline) {log.printf(" External potential uses spline interpolation\n");}
if(sparsegrid) {log.printf(" External potential uses sparse grid\n");}
@@ -151,12 +155,12 @@ void External::calculate()
for(unsigned i=0; i<ncv; ++i) {cv[i]=getArgument(i);}
- double ene=BiasGrid_->getValueAndDerivatives(cv,der);
+ double ene=scale_*BiasGrid_->getValueAndDerivatives(cv,der);
setBias(ene);
for(unsigned i=0; i<ncv; ++i) {
- const double f=-der[i];
+ const double f=-scale_*der[i];
setOutputForce(i,f);
}
}
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index b15f355c6c558a66f53ed40a3671d8eece8ad629..2ed1ce5120f7c6c15dafdb3ca77f56a83f2c91da 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -414,7 +414,6 @@ private:
void readTemperingSpecs(TemperingSpecs &t_specs);
void logTemperingSpecs(const TemperingSpecs &t_specs);
void readGaussians(IFile*);
- bool readChunkOfGaussians(IFile *ifile, unsigned n);
void writeGaussian(const Gaussian&,OFile&);
void addGaussian(const Gaussian&);
double getHeight(const vector<double>&);
@@ -982,8 +981,10 @@ MetaD::MetaD(const ActionOptions& ao):
std::vector<std::string> actualmin=BiasGrid_->getMin();
std::vector<std::string> actualmax=BiasGrid_->getMax();
for(unsigned i=0; i<getNumberOfArguments(); i++) {
- if(gmin[i]!=actualmin[i]) log<<" WARNING: GRID_MIN["<<i<<"] has been adjusted to "<<actualmin[i]<<" to fit periodicity\n";
- if(gmax[i]!=actualmax[i]) log<<" WARNING: GRID_MAX["<<i<<"] has been adjusted to "<<actualmax[i]<<" to fit periodicity\n";
+ std::string is;
+ Tools::convert(i,is);
+ if(gmin[i]!=actualmin[i]) error("GRID_MIN["+is+"] must be adjusted to "+actualmin[i]+" to fit periodicity");
+ if(gmax[i]!=actualmax[i]) error("GRID_MAX["+is+"] must be adjusted to "+actualmax[i]+" to fit periodicity");
}
}
@@ -1234,32 +1235,6 @@ void MetaD::readGaussians(IFile *ifile)
log.printf(" %d Gaussians read\n",nhills);
}
-bool MetaD::readChunkOfGaussians(IFile *ifile, unsigned n)
-{
- unsigned ncv=getNumberOfArguments();
- vector<double> center(ncv);
- vector<double> sigma(ncv);
- double height;
- unsigned nhills=0;
- bool multivariate=false;
- std::vector<Value> tmpvalues;
- for(unsigned j=0; j<getNumberOfArguments(); ++j) tmpvalues.push_back( Value( this, getPntrToArgument(j)->getName(), false ) );
-
- while(scanOneHill(ifile,tmpvalues,center,sigma,height,multivariate)) {
- ;
-// note that for gamma=1 we store directly -F
- if(welltemp_ && biasf_>1.0) height*=(biasf_-1.0)/biasf_;
- addGaussian(Gaussian(center,sigma,height,multivariate));
- if(nhills==n) {
- log.printf(" %u Gaussians read\n",nhills);
- return true;
- }
- nhills++;
- }
- log.printf(" %u Gaussians read\n",nhills);
- return false;
-}
-
void MetaD::writeGaussian(const Gaussian& hill, OFile&file)
{
unsigned ncv=getNumberOfArguments();
@@ -1765,9 +1740,12 @@ bool MetaD::scanOneHill(IFile *ifile, vector<Value> &tmpvalues, vector<double>
}
center[i]=tmpvalues[i].get();
}
+ // scan for kerneltype
+ std::string ktype="gaussian";
+ if( ifile->FieldExist("kerneltype") ) ifile->scanField("kerneltype",ktype);
// scan for multivariate label: record the actual file position so to eventually rewind
- std::string sss, ktype;
- ifile->scanField("multivariate",sss); ifile->scanField("kerneltype",ktype);
+ std::string sss;
+ ifile->scanField("multivariate",sss);
if(sss=="true") multivariate=true;
else if(sss=="false") multivariate=false;
else plumed_merror("cannot parse multivariate = "+ sss);
diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
index 0afc4b75b6d65e5d37d9fb816ef6d848f19fe2af..28fcd042c042d9e608e77506c045da8b4afc33a8 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -268,7 +268,6 @@ private:
unsigned current_value_;
void readGaussians(unsigned iarg, IFile*);
- bool readChunkOfGaussians(unsigned iarg, IFile *ifile, unsigned n);
void writeGaussian(unsigned iarg, const Gaussian&, OFile*);
void addGaussian(unsigned iarg, const Gaussian&);
double getBiasAndDerivatives(unsigned iarg, const vector<double>&, double* der=NULL);
@@ -657,8 +656,10 @@ PBMetaD::PBMetaD(const ActionOptions& ao):
else {BiasGrid_.reset( new SparseGrid(funcl,args,gmin_t,gmax_t,gbin_t,spline,true) );}
std::vector<std::string> actualmin=BiasGrid_->getMin();
std::vector<std::string> actualmax=BiasGrid_->getMax();
- if(gmin_t[0]!=actualmin[0]) log<<" WARNING: GRID_MIN["<<i<<"] has been adjusted to "<<actualmin[0]<<" to fit periodicity\n";
- if(gmax_t[0]!=actualmax[0]) log<<" WARNING: GRID_MAX["<<i<<"] has been adjusted to "<<actualmax[0]<<" to fit periodicity\n";
+ std::string is;
+ Tools::convert(i,is);
+ if(gmin_t[0]!=actualmin[0]) error("GRID_MIN["+is+"] must be adjusted to "+actualmin[0]+" to fit periodicity");
+ if(gmax_t[0]!=actualmax[0]) error("GRID_MAX["+is+"] must be adjusted to "+actualmax[0]+" to fit periodicity");
}
BiasGrids_.emplace_back(std::move(BiasGrid_));
}
@@ -724,6 +725,7 @@ PBMetaD::PBMetaD(const ActionOptions& ao):
ofile->open(ifilesnames[mw_id_*hillsfname.size()+i]);
if(fmt.length()>0) ofile->fmtField(fmt);
ofile->addConstantField("multivariate");
+ ofile->addConstantField("kerneltype");
if(doInt_[i]) {
ofile->addConstantField("lower_int").printField("lower_int",lowI_[i]);
ofile->addConstantField("upper_int").printField("upper_int",uppI_[i]);
@@ -789,35 +791,12 @@ void PBMetaD::readGaussians(unsigned iarg, IFile *ifile)
log.printf(" %d Gaussians read\n",nhills);
}
-bool PBMetaD::readChunkOfGaussians(unsigned iarg, IFile *ifile, unsigned n)
-{
- vector<double> center(1);
- vector<double> sigma(1);
- double height;
- unsigned nhills=0;
- bool multivariate=false;
- std::vector<Value> tmpvalues;
- tmpvalues.push_back( Value( this, getPntrToArgument(iarg)->getName(), false ) );
-
- while(scanOneHill(iarg,ifile,tmpvalues,center,sigma,height,multivariate)) {
- ;
- if(welltemp_) {height*=(biasf_-1.0)/biasf_;}
- addGaussian(iarg, Gaussian(center,sigma,height,multivariate));
- if(nhills==n) {
- log.printf(" %u Gaussians read\n",nhills);
- return true;
- }
- nhills++;
- }
- log.printf(" %u Gaussians read\n",nhills);
- return false;
-}
-
void PBMetaD::writeGaussian(unsigned iarg, const Gaussian& hill, OFile *ofile)
{
ofile->printField("time",getTimeStep()*getStep());
ofile->printField(getPntrToArgument(iarg),hill.center[0]);
+ ofile->printField("kerneltype","gaussian");
if(hill.multivariate) {
ofile->printField("multivariate","true");
double lower = sqrt(1./hill.sigma[0]);
@@ -1160,12 +1139,14 @@ bool PBMetaD::scanOneHill(unsigned iarg, IFile *ifile, vector<Value> &tmpvalues,
}
}
center[0]=tmpvalues[0].get();
+ std::string ktype="gaussian";
+ if( ifile->FieldExist("kerneltype") ) ifile->scanField("kerneltype",ktype);
+
std::string sss;
ifile->scanField("multivariate",sss);
if(sss=="true") multivariate=true;
else if(sss=="false") multivariate=false;
else plumed_merror("cannot parse multivariate = "+ sss);
-
if(multivariate) {
ifile->scanField("sigma_"+getPntrToArgument(iarg)->getName()+"_"+
getPntrToArgument(iarg)->getName(),sigma[0]);
diff --git a/src/bias/ReweightTemperature.cpp b/src/bias/ReweightTemperature.cpp
index 6c219bbf1a67d4157703e9710313c1a5aab2854b..58fddca2c7e1a8c35830e14f7b82fb1d294c6369 100644
--- a/src/bias/ReweightTemperature.cpp
+++ b/src/bias/ReweightTemperature.cpp
@@ -48,12 +48,12 @@ The \ref HISTOGRAM as a function of the distance between atoms 1 and 2 that woul
had been run at the lower temperature of 300 K is estimated using the data from the higher temperature trajectory and output
to a file.
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
aa: REWEIGHT_TEMP TEMP=500 REWEIGHT_TEMP=300
hB: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1 LOGWEIGHTS=aa
DUMPGRID GRID=hB FILE=histoB
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index 05ad5cf2b5cd56b671b36f49a69212686d575ba7..0839c90a2f2e2d5a7aa872d56b6213168e11668e 100644
--- a/src/cltools/Driver.cpp
+++ b/src/cltools/Driver.cpp
@@ -230,6 +230,7 @@ void Driver<real>::registerKeywords( Keywords& keys ) {
keys.add("optional","--length-units","units for length, either as a string or a number");
keys.add("optional","--mass-units","units for mass in pdb and mc file, either as a string or a number");
keys.add("optional","--charge-units","units for charge in pdb and mc file, either as a string or a number");
+ keys.add("optional","--kt","set kBT, it will not be necessary to specify temperature in input file");
keys.add("optional","--dump-forces","dump the forces on a file");
keys.add("optional","--dump-forces-fmt","( default=%%f ) the format to use to dump the forces");
keys.addFlag("--dump-full-virial",false,"with --dump-forces, it dumps the 9 components of the virial");
@@ -248,7 +249,7 @@ void Driver<real>::registerKeywords( Keywords& keys ) {
#ifdef __PLUMED_HAS_MOLFILE_PLUGINS
MOLFILE_INIT_ALL
MOLFILE_REGISTER_ALL(NULL, register_cb)
- for(int i=0; i<plugins.size(); i++) {
+ for(unsigned i=0; i<plugins.size(); i++) {
string kk="--mf_"+string(plugins[i]->name);
string mm=" molfile: the trajectory in "+string(plugins[i]->name)+" format " ;
//cerr<<"REGISTERING "<<kk<<mm<<endl;
@@ -351,6 +352,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
if( debugforces!="" && (debug_dd || debug_pd) ) error("cannot debug forces and domain/particle decomposition at same time");
if( debugforces!="" && sizeof(real)!=sizeof(double) ) error("cannot debug forces in single precision mode");
+ real kt=-1.0;
+ parse("--kt",kt);
string trajectory_fmt;
bool use_molfile=false;
@@ -380,7 +383,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
parse("--itrr",traj_trr);
#endif
#ifdef __PLUMED_HAS_MOLFILE_PLUGINS
- for(int i=0; i<plugins.size(); i++) {
+ for(unsigned i=0; i<plugins.size(); i++) {
string molfile_key="--mf_"+string(plugins[i]->name);
string traj_molfile;
parse(molfile_key,traj_molfile);
@@ -633,6 +636,9 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
natoms=0;
}
if( checknatoms<0 ) {
+ if(kt>=0) {
+ p.cmd("setKbT",&kt);
+ }
checknatoms=natoms;
p.cmd("setNatoms",&natoms);
p.cmd("init");
@@ -731,7 +737,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
}
// info on coords
// the order is xyzxyz...
- for(unsigned i=0; i<3*natoms; i++) {
+ for(int i=0; i<3*natoms; i++) {
coordinates[i]=real(ts_in.coords[i]/10.); //convert to nm
//cerr<<"COOR "<<coordinates[i]<<endl;
}
@@ -750,7 +756,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc) {
if(ret==exdrENDOFFILE) break;
if(ret!=exdrOK) break;
for(unsigned i=0; i<3; i++) for(unsigned j=0; j<3; j++) cell[3*i+j]=box[i][j];
- for(unsigned i=0; i<natoms; i++) for(unsigned j=0; j<3; j++)
+ for(int i=0; i<natoms; i++) for(unsigned j=0; j<3; j++)
coordinates[3*i+j]=real(pos[i][j]);
#endif
} else {
diff --git a/src/cltools/pesmd.cpp b/src/cltools/pesmd.cpp
index 1b6a0733cf376d209bb012664c2d0d526da19d3b..0baa1807c9f8d8fd8ac0c56c66da17543acd27d5 100755
--- a/src/cltools/pesmd.cpp
+++ b/src/cltools/pesmd.cpp
@@ -128,7 +128,7 @@ private:
void read_input(double& temperature,
double& tstep,
double& friction,
- int& dim,
+ int& dim,
std::string& plumedin,
std::vector<double>& ipos,
int& nstep,
@@ -155,7 +155,7 @@ private:
std::vector<double> min( dim ); parseVector("min",min);
std::vector<double> max( dim ); parseVector("max",max);
periods.resize( dim );
- for(unsigned i=0; i<dim; ++i) {
+ for(int i=0; i<dim; ++i) {
if( max[i]<min[i] ) error("invalid periods specified max is less than min");
periods[i]=max[i]-min[i];
}
@@ -197,21 +197,21 @@ public:
plumed->cmd("init");
// Now create some fake atoms
- unsigned nat = std::floor( dim/3 ) + 1;
+ int nat = std::floor( dim/3 ) + 1;
std::vector<double> masses( 1+nat, 1 );
std::vector<Vector> velocities( nat ), positions( nat+1 ), forces( nat+1 );
// Will set these properly eventually
- unsigned k=0; positions[0].zero(); // Atom zero is fixed at origin
- for(unsigned i=0; i<nat; ++i) for(unsigned j=0; j<3; ++j) {
+ int k=0; positions[0].zero(); // Atom zero is fixed at origin
+ for(int i=0; i<nat; ++i) for(unsigned j=0; j<3; ++j) {
if( k<dim ) { positions[1+i][j]=ipos[k]; } else { positions[1+i][j]=0;}
k++;
}
// And initialize the velocities
- for(unsigned i=0; i<nat; ++i) for(unsigned j=0; j<3; ++j) velocities[i][j]=random.Gaussian() * sqrt( temp );
+ for(int i=0; i<nat; ++i) for(int j=0; j<3; ++j) velocities[i][j]=random.Gaussian() * sqrt( temp );
// And calcualte the kinetic energy
double tke=0;
- for(unsigned i=0; i<nat; ++i) {
- for(unsigned j=0; j<3; ++j) {
+ for(int i=0; i<nat; ++i) {
+ for(int j=0; j<3; ++j) {
if( 3*i+j>dim ) break;
tke += 0.5*velocities[i][j]*velocities[i][j];
}
@@ -229,22 +229,18 @@ public:
plumed->cmd("calc");
-// potential=calc_energy(positions,forces);
double therm_eng=0;
-
FILE* fp=fopen("stats.out","w+");
-// double conserved = potential+1.5*ttt+therm_eng; FILE* fp=fopen("stats.out","w+");
-// if( pc.Get_rank()==0 ) fprintf(fp,"%d %f %f \n", 0, 0., tke, therm_eng );
- for(unsigned istep=0; istep<nsteps; ++istep) {
+ for(int istep=0; istep<nsteps; ++istep) {
- if( istep%20==0 && pc.Get_rank()==0 ) printf("Doing step %u\n",istep);
+ if( istep%20==0 && pc.Get_rank()==0 ) printf("Doing step %i\n",istep);
// Langevin thermostat
double lscale=exp(-0.5*tstep/friction);
double lrand=sqrt((1.-lscale*lscale)*temp);
- for(unsigned j=0; j<nat; ++j) {
- for(unsigned k=0; k<3; ++k) {
+ for(int j=0; j<nat; ++j) {
+ for(int k=0; k<3; ++k) {
if( 3*j+k>dim ) break;
therm_eng=therm_eng+0.5*velocities[j][k]*velocities[j][k];
velocities[j][k]=lscale*velocities[j][k]+lrand*random.Gaussian();
@@ -253,14 +249,11 @@ public:
}
// First step of velocity verlet
- for(unsigned j=0; j<nat; ++j) {
- for(unsigned k=0; k<3; ++k) {
+ for(int j=0; j<nat; ++j) {
+ for(int k=0; k<3; ++k) {
if( 3*j+k>dim ) break;
velocities[j][k] = velocities[j][k] + 0.5*tstep*forces[1+j][k];
positions[1+j][k] = positions[1+j][k] + tstep*velocities[j][k];
- // Apply pbc
- // if( positions[0][k]>pi ) positions[0][k]-=2*pi;
- // if( positions[0][k]<=-pi ) positions[0][k]+=2*pi;
}
}
@@ -279,8 +272,8 @@ public:
if(plumedWantsToStop) nsteps=istep;
// Second step of velocity verlet
- for(unsigned j=0; j<nat; ++j) {
- for(unsigned k=0; k<3; ++k) {
+ for(int j=0; j<nat; ++j) {
+ for(int k=0; k<3; ++k) {
if( 3*j+k>dim ) break;
velocities[j][k] = velocities[j][k] + 0.5*tstep*forces[1+j][k];
}
@@ -289,8 +282,8 @@ public:
// Langevin thermostat
lscale=exp(-0.5*tstep/friction);
lrand=sqrt((1.-lscale*lscale)*temp);
- for(unsigned j=0; j<nat; ++j) {
- for(unsigned k=0; k<3; ++k) {
+ for(int j=0; j<nat; ++j) {
+ for(int k=0; k<3; ++k) {
if( 3*j+k>dim ) break;
therm_eng=therm_eng+0.5*velocities[j][k]*velocities[j][k];
velocities[j][k]=lscale*velocities[j][k]+lrand*random.Gaussian();
@@ -299,8 +292,8 @@ public:
}
// Calculate total kinetic energy
tke=0;
- for(unsigned i=0; i<nat; ++i) {
- for(unsigned j=0; j<3; ++j) {
+ for(int i=0; i<nat; ++i) {
+ for(int j=0; j<3; ++j) {
if( 3*i+j>dim ) break;
tke += 0.5*velocities[i][j]*velocities[i][j];
}
@@ -308,7 +301,7 @@ public:
// Print everything
// conserved = potential+1.5*ttt+therm_eng;
- if( pc.Get_rank()==0 ) fprintf(fp,"%u %f %f %f \n", istep, istep*tstep, tke, therm_eng );
+ if( pc.Get_rank()==0 ) fprintf(fp,"%i %f %f %f \n", istep, istep*tstep, tke, therm_eng );
}
fclose(fp);
diff --git a/src/colvar/CoordinationBase.cpp b/src/colvar/CoordinationBase.cpp
index cf4f793f5559af6ee38ba53d127287ed77c3575c..996bd5970c94f364b7f03ba37de11319eb5bf59d 100644
--- a/src/colvar/CoordinationBase.cpp
+++ b/src/colvar/CoordinationBase.cpp
@@ -195,7 +195,7 @@ void CoordinationBase::calculate()
}
#pragma omp critical
if(nt>1) {
- for(int i=0; i<getPositions().size(); i++) deriv[i]+=omp_deriv[i];
+ for(unsigned i=0; i<getPositions().size(); i++) deriv[i]+=omp_deriv[i];
virial+=omp_virial;
}
}
diff --git a/src/colvar/DRMSD.cpp b/src/colvar/DRMSD.cpp
index 826df88cc897f293ff8fe91a365992982dec886d..8693fa2cb4bc7aacdae41dd8570226c3b6353c62 100644
--- a/src/colvar/DRMSD.cpp
+++ b/src/colvar/DRMSD.cpp
@@ -46,7 +46,7 @@ often cheaper and easier to calculate the distances between all the pairs of ato
between the two structures, \f$\mathbf{X}^a\f$ and \f$\mathbf{X}^b\f$ can then be measured as:
\f[
-d(\mathbf{X}^A, \mathbf{X}^B) = \frac{1}{N(N-1)} \sum_{i \ne j} [ d(\mathbf{x}_i^a,\mathbf{x}_j^a) - d(\mathbf{x}_i^b,\mathbf{x}_j^b) ]^2
+d(\mathbf{X}^A, \mathbf{X}^B) = \sqrt{\frac{1}{N(N-1)} \sum_{i \ne j} [ d(\mathbf{x}_i^a,\mathbf{x}_j^a) - d(\mathbf{x}_i^b,\mathbf{x}_j^b) ]^2}
\f]
where \f$N\f$ is the number of atoms and \f$d(\mathbf{x}_i,\mathbf{x}_j)\f$ represents the distance between
diff --git a/src/colvar/ERMSD.cpp b/src/colvar/ERMSD.cpp
index 60616e23a13b3aab678a59514baf513066b7d82b..fc99b888c7787278b91beb906cd678cac83f35d0 100644
--- a/src/colvar/ERMSD.cpp
+++ b/src/colvar/ERMSD.cpp
@@ -55,12 +55,13 @@ eRMSD measures the distance between structures by considering only the relative
2. Calculate all pairwise distance vectors \f$ \vec{r}_{i,j} \f$ among base centers.
-3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where \f$ a=b=5 \AA, c= 3 \AA\f$. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions.
+3. Rescale distance vectors as \f$ \tilde{\vec{r}}_{i,j} = (r_x/a,r_y/a,r_z/b) \f$, where a=b=5 \AA, c= 3 \AA. This rescaling has the effect of weghting more deviations on the z-axis with respect to the x/y directions.
4. Calculate the G vectors
\f[
-\vec{G}(\tilde{\vec{r}}) = (\sin(\gamma \tilde{r}) \tilde{r}_x/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_y/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_z/\tilde{r}, 1+\cos(\gamma \tilde{r})) \times \Theta(\tilde{r}_{cutoff}-\tilde{r})
+\vec{G}(\tilde{\vec{r}}) = (\sin(\gamma \tilde{r}) \tilde{r}_x/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_y/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_z/\tilde{r}, 1+\cos(\gamma \tilde{r})) \times
+\frac{\Theta(\tilde{r}_{cutoff}-\tilde{r})}{\gamma}
\f]
Here, \f$ \gamma = \pi/\tilde{r}_{cutoff}\f$ and \f$ \Theta \f$ is the Heaviside step function. The default cutoff is set to 2.4.
@@ -176,7 +177,7 @@ ERMSD::ERMSD(const ActionOptions&ao):
// shift to count from zero
for(unsigned i=0; i<pairs_.size(); ++i) pairs_[i]--;
- ermsd.setReference(reference_positions,pairs_,cutoff);
+ ermsd.setReference(reference_positions,pairs_,cutoff/atoms.getUnits().getLength());
requestAtoms(atoms_);
derivs.resize(natoms);
@@ -204,9 +205,10 @@ void ERMSD::calculate() {
// Notice that this might have problems when having 2 RNA molecules (hybridization).
ermsdist=ermsd.calculate(getPositions(),fake_pbc,derivs,virial);
- setValue(ermsdist);
+ const double scale=atoms.getUnits().getLength();
+ setValue(ermsdist*scale);
- for(unsigned i=0; i<derivs.size(); ++i) {setAtomsDerivatives(i,derivs[i]);}
+ for(unsigned i=0; i<derivs.size(); ++i) {setAtomsDerivatives(i,derivs[i]*scale);}
setBoxDerivativesNoPbc();
diff --git a/src/colvar/Fake.cpp b/src/colvar/Fake.cpp
index c9ac270586c97113085f01fd834abe97f5a28afa..d942a4c40830990fac9c1a833be1236df944ee0b 100644
--- a/src/colvar/Fake.cpp
+++ b/src/colvar/Fake.cpp
@@ -62,7 +62,7 @@ void ColvarFake::registerKeywords( Keywords& keys ) {
keys.add("atoms","ATOMS","the fake atom index, a number is enough");
keys.reserve("compulsory","PERIODIC","if the output of your function is periodic then you should specify the periodicity of the function. If the output is not periodic you must state this using PERIODIC=NO,NO (one for the lower and the other for the upper boundary). For multicomponents then it is PERIODIC=mincomp1,maxcomp1,mincomp2,maxcomp2 etc ");
keys.use("PERIODIC");
- keys.add("optional","COMPONENTS","additional componnets that this variable is supposed to have. Periodicity is ruled by PERIODIC keyword ");
+ keys.add("optional","COMPONENTS","additional components that this variable is supposed to have. Periodicity is ruled by PERIODIC keyword ");
}
ColvarFake::ColvarFake(const ActionOptions&ao):
@@ -86,7 +86,7 @@ ColvarFake::ColvarFake(const ActionOptions&ao):
std::vector<std::string> period;
parseVector("PERIODIC",period);
if(period.size()!=0) {
- plumed_massert(getNumberOfComponents()*2==period.size(),"the periodicty should coincide with the number of components");
+ plumed_massert(static_cast<unsigned>(getNumberOfComponents()*2)==period.size(),"the periodicty should coincide with the number of components");
if(comps.size()!=0) {
for(int i=0; i<getNumberOfComponents(); i++) {
string pp=comps[i];
diff --git a/src/colvar/Gyration.cpp b/src/colvar/Gyration.cpp
index f811b21ca6a968e473b73789213810848a00c61a..e5b8b5f84c57ee3e69e3aec4b1bc47bf04b83f65 100644
--- a/src/colvar/Gyration.cpp
+++ b/src/colvar/Gyration.cpp
@@ -145,7 +145,8 @@ Gyration::Gyration(const ActionOptions&ao):
case GYRATION_2: log.printf(" THE MIDDLE PRINCIPAL RADIUS OF GYRATION (r_g2);"); break;
case GYRATION_1: log.printf(" THE LARGEST PRINCIPAL RADIUS OF GYRATION (r_g1);"); break;
}
- if(rg_type>TRACE) log<<" Bibliography "<<plumed.cite("JiriÌ Vymetal and JiriÌ Vondrasek, J. Phys. Chem. A 115, 11455 (2011)"); log<<"\n";
+ if(rg_type>TRACE) log<<" Bibliography "<<plumed.cite("JiriÌ Vymetal and JiriÌ Vondrasek, J. Phys. Chem. A 115, 11455 (2011)");
+ log<<"\n";
log.printf(" atoms involved : ");
for(unsigned i=0; i<atoms.size(); ++i) {
diff --git a/src/colvar/PCARMSD.cpp b/src/colvar/PCARMSD.cpp
index 72cc3d2e5cbd43534aad04c88be4c84c5b074700..c0c7f4f9563ef2832227fbfac659d355f5b4b138 100644
--- a/src/colvar/PCARMSD.cpp
+++ b/src/colvar/PCARMSD.cpp
@@ -208,7 +208,7 @@ void PCARMSD::calculate() {
}
}
- for(unsigned i=0; i<getNumberOfComponents(); ++i) setBoxDerivativesNoPbc( getPntrToComponent(i) );
+ for(int i=0; i<getNumberOfComponents(); ++i) setBoxDerivativesNoPbc( getPntrToComponent(i) );
}
diff --git a/src/colvar/PathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
index c244708d5daf79ba4de2f602fab816771d5bbb7b..6c89518de8ae6f47bc71bb97fdc1b53c0f297682 100644
--- a/src/colvar/PathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -50,11 +50,11 @@ PathMSDBase::PathMSDBase(const ActionOptions&ao):
PLUMED_COLVAR_INIT(ao),
neigh_size(-1),
neigh_stride(-1),
- nframes(0),
epsilonClose(-1),
debugClose(0),
logClose(0),
- computeRefClose(false)
+ computeRefClose(false),
+ nframes(0)
{
parse("LAMBDA",lambda);
parse("NEIGH_SIZE",neigh_size);
@@ -84,12 +84,10 @@ PathMSDBase::PathMSDBase(const ActionOptions&ao):
if(aaa!=mypdb.getAtomNumbers()) error("frames should contain same atoms in same order");
log<<"Found PDB: "<<nframes<<" containing "<<mypdb.getAtomNumbers().size()<<" atoms\n";
pdbv.push_back(mypdb);
-// requestAtoms(mypdb.getAtomNumbers()); // is done in non base classes
derivs_s.resize(mypdb.getAtomNumbers().size());
derivs_z.resize(mypdb.getAtomNumbers().size());
mymsd.set(mypdb,"OPTIMAL");
msdv.push_back(mymsd); // the vector that stores the frames
- //log<<mypdb;
} else {break ;}
}
fclose (fp);
@@ -139,7 +137,7 @@ void PathMSDBase::calculate() {
// resize the list to full
if(imgVec.empty()) { // this is the signal that means: recalculate all
imgVec.resize(nframes);
-#pragma simd
+ #pragma omp simd
for(unsigned i=0; i<nframes; i++) {
imgVec[i].property=indexvec[i];
imgVec[i].index=i;
@@ -170,7 +168,6 @@ void PathMSDBase::calculate() {
// and we need to accurately recalculate for all reference structures
computeRefClose = true;
imgVec.resize(nframes);
-#pragma simd
for(unsigned i=0; i<nframes; i++) {
imgVec[i].property=indexvec[i];
imgVec[i].index=i;
@@ -197,7 +194,7 @@ void PathMSDBase::calculate() {
for(unsigned i=rank; i<imgVec.size(); i+=stride) {
tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);
plumed_assert(tmp_derivs.size()==nat);
-#pragma simd
+ #pragma omp simd
for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
}
}
@@ -206,7 +203,7 @@ void PathMSDBase::calculate() {
for(unsigned i=rank; i<imgVec.size(); i+=stride) {
tmp_distances[i] = msdv[imgVec[i].index].calculateWithCloseStructure(getPositions(), tmp_derivs, rotationPosClose, rotationRefClose[imgVec[i].index], drotationPosCloseDrr01, true);
plumed_assert(tmp_derivs.size()==nat);
-#pragma simd
+ #pragma omp simd
for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
if (debugClose) {
double withclose = tmp_distances[i];
@@ -226,7 +223,7 @@ void PathMSDBase::calculate() {
for(unsigned i=rank; i<imgVec.size(); i+=stride) {
tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);
plumed_assert(tmp_derivs.size()==nat);
-#pragma simd
+ #pragma omp simd
for(unsigned j=0; j<nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];
}
}
@@ -275,17 +272,18 @@ void PathMSDBase::calculate() {
val_z_path->set(-(1./lambda)*std::log(partition));
for(unsigned j=0; j<s_path.size(); j++) {
// clean up
-#pragma simd
+ #pragma omp simd
for(unsigned i=0; i< derivs_s.size(); i++) {derivs_s[i].zero();}
// do the derivative
-#pragma simd
for(const auto & it : imgVec) {
double expval=it.similarity;
tmp=lambda*expval*(s_path[j]-it.property[j])/partition;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i< derivs_s.size(); i++) { derivs_s[i]+=tmp*it.distder[i] ;}
-#pragma ivdep
- if(j==0) {for(unsigned i=0; i< derivs_z.size(); i++) { derivs_z[i]+=it.distder[i]*expval/partition;}}
+ if(j==0) {
+ #pragma omp simd
+ for(unsigned i=0; i< derivs_z.size(); i++) { derivs_z[i]+=it.distder[i]*expval/partition;}
+ }
}
for(unsigned i=0; i< derivs_s.size(); i++) {
setAtomsDerivatives (val_s_path[j],i,derivs_s[i]);
diff --git a/src/core/ActionAtomistic.cpp b/src/core/ActionAtomistic.cpp
index cfb16c8fd165f0038f91715e5fed800ec1b3de3e..b6058e9e9e51cad521d9beb2e4babfabd34ac21d 100644
--- a/src/core/ActionAtomistic.cpp
+++ b/src/core/ActionAtomistic.cpp
@@ -44,7 +44,6 @@ ActionAtomistic::~ActionAtomistic() {
ActionAtomistic::ActionAtomistic(const ActionOptions&ao):
Action(ao),
- pbc_fwd(new(Pbc)),
lockRequestAtoms(false),
donotretrieve(false),
donotforce(false),
diff --git a/src/core/Atoms.cpp b/src/core/Atoms.cpp
index b63c8e5d15729503975cc98d2aa62c69aca2f49a..8766b0d7765d76450b955322bc95785600a9fc1d 100644
--- a/src/core/Atoms.cpp
+++ b/src/core/Atoms.cpp
@@ -41,7 +41,6 @@ class PlumedMain;
Atoms::Atoms(PlumedMain&plumed):
natoms(0),
- pbc_fwd(new Pbc),
md_energy(0.0),
energy(0.0),
dataCanBeSet(false),
diff --git a/src/core/CLToolMain.cpp b/src/core/CLToolMain.cpp
index 0ac15965db5480ccdeb9c8737151220e1d07ac61..d422dda926ba11fa999fe04078163902a447adaf 100644
--- a/src/core/CLToolMain.cpp
+++ b/src/core/CLToolMain.cpp
@@ -54,8 +54,7 @@ const std::unordered_map<std::string, int> & clToolMainWordMap() {
CLToolMain::CLToolMain():
argc(0),
in(stdin),
- out(stdout),
- comm_fwd(new Communicator)
+ out(stdout)
{
}
diff --git a/src/core/ExchangePatterns.cpp b/src/core/ExchangePatterns.cpp
index 6da42b123ca17fd056d8847b71f03b7e235e31b6..9f55d55bc9e1c8b340859d9ca20feed6897a220f 100644
--- a/src/core/ExchangePatterns.cpp
+++ b/src/core/ExchangePatterns.cpp
@@ -28,8 +28,7 @@ namespace PLMD {
ExchangePatterns::ExchangePatterns():
PatternFlag(NONE),
- NumberOfReplicas(1),
- random_fwd(new Random)
+ NumberOfReplicas(1)
{}
ExchangePatterns::~ExchangePatterns() {
diff --git a/src/core/GREX.cpp b/src/core/GREX.cpp
index 4476e8a9df8ec3325cf1be5a3d9de9aef069103a..d71475847791a39a15c183e7b179246951fa9c4d 100644
--- a/src/core/GREX.cpp
+++ b/src/core/GREX.cpp
@@ -44,8 +44,6 @@ const std::unordered_map<std::string, int> & GREXWordMap() {
GREX::GREX(PlumedMain&p):
initialized(false),
- intracomm_fwd(new Communicator),
- intercomm_fwd(new Communicator),
plumedMain(p),
atoms(p.getAtoms()),
partner(-1), // = unset
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index 0769bd196a0aea20166f43c939560585f1f4e394..389b99cf1feaeb309b7129eb66a9ead4775cc36e 100644
--- a/src/core/PlumedMain.cpp
+++ b/src/core/PlumedMain.cpp
@@ -63,22 +63,15 @@ const std::unordered_map<std::string, int> & plumedMainWordMap() {
}
PlumedMain::PlumedMain():
- comm_fwd(new Communicator),
- multi_sim_comm_fwd(new Communicator),
- dlloader_fwd(new DLLoader),
- stopwatch_fwd(new Stopwatch),
initialized(false),
- log_fwd(new Log),
- citations_fwd(new Citations),
step(0),
active(false),
mydatafetcher(DataFetchingObject::create(sizeof(double),*this)),
endPlumed(false),
- atoms_fwd(new Atoms(*this)),
- actionSet_fwd(new ActionSet(*this)),
+ atoms_fwd(*this),
+ actionSet_fwd(*this),
bias(0.0),
work(0.0),
- exchangePatterns_fwd(new(ExchangePatterns)),
exchangeStep(false),
restart(false),
doCheckPoint(false),
@@ -109,377 +102,389 @@ PlumedMain::~PlumedMain() {
void PlumedMain::cmd(const std::string & word,void*val) {
- stopwatch.start();
-
- std::vector<std::string> words=Tools::getWords(word);
- unsigned nw=words.size();
- if(nw==0) {
- // do nothing
- } else {
- int iword=-1;
- double d;
- const auto it=plumedMainWordMap().find(words[0]);
- if(it!=plumedMainWordMap().end()) iword=it->second;
- switch(iword) {
- case cmd_setBox:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setBox(val);
- break;
- case cmd_setPositions:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val);
- break;
- case cmd_setMasses:
- CHECK_INIT(initialized,word);
- atoms.setMasses(val);
- break;
- case cmd_setCharges:
- CHECK_INIT(initialized,word);
- atoms.setCharges(val);
- break;
- case cmd_setPositionsX:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,0);
- break;
- case cmd_setPositionsY:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,1);
- break;
- case cmd_setPositionsZ:
- CHECK_INIT(initialized,word);
- atoms.setPositions(val,2);
- break;
- case cmd_setVirial:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setVirial(val);
- break;
- case cmd_setEnergy:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setEnergy(val);
- break;
- case cmd_setForces:
- CHECK_INIT(initialized,word);
- atoms.setForces(val);
- break;
- case cmd_setForcesX:
- CHECK_INIT(initialized,word);
- atoms.setForces(val,0);
- break;
- case cmd_setForcesY:
- CHECK_INIT(initialized,word);
- atoms.setForces(val,1);
- break;
- case cmd_setForcesZ:
- CHECK_INIT(initialized,word);
- atoms.setForces(val,2);
- break;
- case cmd_calc:
- CHECK_INIT(initialized,word);
- calc();
- break;
- case cmd_prepareDependencies:
- CHECK_INIT(initialized,word);
- prepareDependencies();
- break;
- case cmd_shareData:
- CHECK_INIT(initialized,word);
- shareData();
- break;
- case cmd_prepareCalc:
- CHECK_INIT(initialized,word);
- prepareCalc();
- break;
- case cmd_performCalc:
- CHECK_INIT(initialized,word);
- performCalc();
- break;
- case cmd_performCalcNoUpdate:
- CHECK_INIT(initialized,word);
- performCalcNoUpdate();
- break;
- case cmd_update:
- CHECK_INIT(initialized,word);
- update();
- break;
- case cmd_setStep:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- step=(*static_cast<int*>(val));
- atoms.startStep();
- break;
- case cmd_setStepLong:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- step=(*static_cast<long int*>(val));
- atoms.startStep();
- break;
- // words used less frequently:
- case cmd_setAtomsNlocal:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setAtomsNlocal(*static_cast<int*>(val));
- break;
- case cmd_setAtomsGatindex:
- CHECK_INIT(initialized,word);
- atoms.setAtomsGatindex(static_cast<int*>(val),false);
- break;
- case cmd_setAtomsFGatindex:
- CHECK_INIT(initialized,word);
- atoms.setAtomsGatindex(static_cast<int*>(val),true);
- break;
- case cmd_setAtomsContiguous:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setAtomsContiguous(*static_cast<int*>(val));
- break;
- case cmd_createFullList:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.createFullList(static_cast<int*>(val));
- break;
- case cmd_getFullList:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.getFullList(static_cast<int**>(val));
- break;
- case cmd_clearFullList:
- CHECK_INIT(initialized,word);
- atoms.clearFullList();
- break;
- /* ADDED WITH API==6 */
- case cmd_getDataRank:
- CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
- if( nw==2 ) DataFetchingObject::get_rank( actionSet, words[1], "", static_cast<long*>(val) );
- else DataFetchingObject::get_rank( actionSet, words[1], words[2], static_cast<long*>(val) );
- break;
- /* ADDED WITH API==6 */
- case cmd_getDataShape:
- CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
- if( nw==2 ) DataFetchingObject::get_shape( actionSet, words[1], "", static_cast<long*>(val) );
- else DataFetchingObject::get_shape( actionSet, words[1], words[2], static_cast<long*>(val) );
- break;
- /* ADDED WITH API==6 */
- case cmd_setMemoryForData:
- CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
- if( nw==2 ) mydatafetcher->setData( words[1], "", val );
- else mydatafetcher->setData( words[1], words[2], val );
- break;
- case cmd_read:
- CHECK_INIT(initialized,word);
- if(val)readInputFile(static_cast<char*>(val));
- else readInputFile("plumed.dat");
- break;
- case cmd_readInputLine:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- readInputLine(static_cast<char*>(val));
- break;
- case cmd_clear:
- CHECK_INIT(initialized,word);
- actionSet.clearDelete();
- break;
- case cmd_getApiVersion:
- CHECK_NOTNULL(val,word);
- *(static_cast<int*>(val))=6;
- break;
- // commands which can be used only before initialization:
- case cmd_init:
- CHECK_NOTINIT(initialized,word);
- init();
- break;
- case cmd_setRealPrecision:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setRealPrecision(*static_cast<int*>(val));
- mydatafetcher=DataFetchingObject::create(*static_cast<int*>(val),*this);
- break;
- case cmd_setMDLengthUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDLengthUnits(d);
- break;
- case cmd_setMDChargeUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDChargeUnits(d);
- break;
- case cmd_setMDMassUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDMassUnits(d);
- break;
- case cmd_setMDEnergyUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDEnergyUnits(d);
- break;
- case cmd_setMDTimeUnits:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.MD2double(val,d);
- atoms.setMDTimeUnits(d);
- break;
- case cmd_setNaturalUnits:
- // set the boltzman constant for MD in natural units (kb=1)
- // only needed in LJ codes if the MD is passing temperatures to plumed (so, not yet...)
- // use as cmd("setNaturalUnits")
- CHECK_NOTINIT(initialized,word);
- atoms.setMDNaturalUnits(true);
- break;
- case cmd_setNoVirial:
- CHECK_NOTINIT(initialized,word);
- novirial=true;
- break;
- case cmd_setPlumedDat:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- plumedDat=static_cast<char*>(val);
- break;
- case cmd_setMPIComm:
- CHECK_NOTINIT(initialized,word);
- comm.Set_comm(val);
- atoms.setDomainDecomposition(comm);
- break;
- case cmd_setMPIFComm:
- CHECK_NOTINIT(initialized,word);
- comm.Set_fcomm(val);
- atoms.setDomainDecomposition(comm);
- break;
- case cmd_setMPImultiSimComm:
- CHECK_NOTINIT(initialized,word);
- multi_sim_comm.Set_comm(val);
- break;
- case cmd_setNatoms:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setNatoms(*static_cast<int*>(val));
- break;
- case cmd_setTimestep:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setTimeStep(val);
- break;
- /* ADDED WITH API==2 */
- case cmd_setKbT:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.setKbT(val);
- break;
- /* ADDED WITH API==3 */
- case cmd_setRestart:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- if(*static_cast<int*>(val)!=0) restart=true;
- break;
- /* ADDED WITH API==4 */
- case cmd_doCheckPoint:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- doCheckPoint = false;
- if(*static_cast<int*>(val)!=0) doCheckPoint = true;
- break;
- /* STOP API */
- case cmd_setMDEngine:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- MDEngine=static_cast<char*>(val);
- break;
- case cmd_setLog:
- CHECK_NOTINIT(initialized,word);
- log.link(static_cast<FILE*>(val));
- break;
- case cmd_setLogFile:
- CHECK_NOTINIT(initialized,word);
- CHECK_NOTNULL(val,word);
- log.open(static_cast<char*>(val));
- break;
- // other commands that should be used after initialization:
- case cmd_setStopFlag:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- stopFlag=static_cast<int*>(val);
- break;
- case cmd_getExchangesFlag:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.getFlag((*static_cast<int*>(val)));
- break;
- case cmd_setExchangesSeed:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.setSeed((*static_cast<int*>(val)));
- break;
- case cmd_setNumberOfReplicas:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.setNofR((*static_cast<int*>(val)));
- break;
- case cmd_getExchangesList:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- exchangePatterns.getList((static_cast<int*>(val)));
- break;
- case cmd_runFinalJobs:
- CHECK_INIT(initialized,word);
- runJobsAtEndOfCalculation();
- break;
- case cmd_isEnergyNeeded:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- if(atoms.isEnergyNeeded()) *(static_cast<int*>(val))=1;
- else *(static_cast<int*>(val))=0;
- break;
- case cmd_getBias:
- CHECK_INIT(initialized,word);
- CHECK_NOTNULL(val,word);
- atoms.double2MD(getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);
- break;
- case cmd_checkAction:
- CHECK_NOTNULL(val,word);
- plumed_assert(nw==2);
- *(static_cast<int*>(val))=(actionRegister().check(words[1]) ? 1:0);
- break;
- case cmd_setExtraCV:
- CHECK_NOTNULL(val,word);
- plumed_assert(nw==2);
- atoms.setExtraCV(words[1],val);
- break;
- case cmd_setExtraCVForce:
- CHECK_NOTNULL(val,word);
- plumed_assert(nw==2);
- atoms.setExtraCVForce(words[1],val);
- break;
- case cmd_GREX:
- if(!grex) grex.reset(new GREX(*this));
- plumed_massert(grex,"error allocating grex");
- {
- std::string kk=words[1];
- for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
- grex->cmd(kk.c_str(),val);
- }
- break;
- case cmd_CLTool:
- CHECK_NOTINIT(initialized,word);
- if(!cltool) cltool.reset(new CLToolMain);
- {
- std::string kk=words[1];
- for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
- cltool->cmd(kk.c_str(),val);
+ try {
+
+ stopwatch.start();
+
+ std::vector<std::string> words=Tools::getWords(word);
+ unsigned nw=words.size();
+ if(nw==0) {
+ // do nothing
+ } else {
+ int iword=-1;
+ double d;
+ const auto it=plumedMainWordMap().find(words[0]);
+ if(it!=plumedMainWordMap().end()) iword=it->second;
+ switch(iword) {
+ case cmd_setBox:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setBox(val);
+ break;
+ case cmd_setPositions:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val);
+ break;
+ case cmd_setMasses:
+ CHECK_INIT(initialized,word);
+ atoms.setMasses(val);
+ break;
+ case cmd_setCharges:
+ CHECK_INIT(initialized,word);
+ atoms.setCharges(val);
+ break;
+ case cmd_setPositionsX:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,0);
+ break;
+ case cmd_setPositionsY:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,1);
+ break;
+ case cmd_setPositionsZ:
+ CHECK_INIT(initialized,word);
+ atoms.setPositions(val,2);
+ break;
+ case cmd_setVirial:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setVirial(val);
+ break;
+ case cmd_setEnergy:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setEnergy(val);
+ break;
+ case cmd_setForces:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val);
+ break;
+ case cmd_setForcesX:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,0);
+ break;
+ case cmd_setForcesY:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,1);
+ break;
+ case cmd_setForcesZ:
+ CHECK_INIT(initialized,word);
+ atoms.setForces(val,2);
+ break;
+ case cmd_calc:
+ CHECK_INIT(initialized,word);
+ calc();
+ break;
+ case cmd_prepareDependencies:
+ CHECK_INIT(initialized,word);
+ prepareDependencies();
+ break;
+ case cmd_shareData:
+ CHECK_INIT(initialized,word);
+ shareData();
+ break;
+ case cmd_prepareCalc:
+ CHECK_INIT(initialized,word);
+ prepareCalc();
+ break;
+ case cmd_performCalc:
+ CHECK_INIT(initialized,word);
+ performCalc();
+ break;
+ case cmd_performCalcNoUpdate:
+ CHECK_INIT(initialized,word);
+ performCalcNoUpdate();
+ break;
+ case cmd_update:
+ CHECK_INIT(initialized,word);
+ update();
+ break;
+ case cmd_setStep:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ step=(*static_cast<int*>(val));
+ atoms.startStep();
+ break;
+ case cmd_setStepLong:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ step=(*static_cast<long int*>(val));
+ atoms.startStep();
+ break;
+ // words used less frequently:
+ case cmd_setAtomsNlocal:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setAtomsNlocal(*static_cast<int*>(val));
+ break;
+ case cmd_setAtomsGatindex:
+ CHECK_INIT(initialized,word);
+ atoms.setAtomsGatindex(static_cast<int*>(val),false);
+ break;
+ case cmd_setAtomsFGatindex:
+ CHECK_INIT(initialized,word);
+ atoms.setAtomsGatindex(static_cast<int*>(val),true);
+ break;
+ case cmd_setAtomsContiguous:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setAtomsContiguous(*static_cast<int*>(val));
+ break;
+ case cmd_createFullList:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.createFullList(static_cast<int*>(val));
+ break;
+ case cmd_getFullList:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.getFullList(static_cast<int**>(val));
+ break;
+ case cmd_clearFullList:
+ CHECK_INIT(initialized,word);
+ atoms.clearFullList();
+ break;
+ /* ADDED WITH API==6 */
+ case cmd_getDataRank:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) DataFetchingObject::get_rank( actionSet, words[1], "", static_cast<long*>(val) );
+ else DataFetchingObject::get_rank( actionSet, words[1], words[2], static_cast<long*>(val) );
+ break;
+ /* ADDED WITH API==6 */
+ case cmd_getDataShape:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) DataFetchingObject::get_shape( actionSet, words[1], "", static_cast<long*>(val) );
+ else DataFetchingObject::get_shape( actionSet, words[1], words[2], static_cast<long*>(val) );
+ break;
+ /* ADDED WITH API==6 */
+ case cmd_setMemoryForData:
+ CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);
+ if( nw==2 ) mydatafetcher->setData( words[1], "", val );
+ else mydatafetcher->setData( words[1], words[2], val );
+ break;
+ case cmd_read:
+ CHECK_INIT(initialized,word);
+ if(val)readInputFile(static_cast<char*>(val));
+ else readInputFile("plumed.dat");
+ break;
+ case cmd_readInputLine:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ readInputLine(static_cast<char*>(val));
+ break;
+ case cmd_clear:
+ CHECK_INIT(initialized,word);
+ actionSet.clearDelete();
+ break;
+ case cmd_getApiVersion:
+ CHECK_NOTNULL(val,word);
+ *(static_cast<int*>(val))=6;
+ break;
+ // commands which can be used only before initialization:
+ case cmd_init:
+ CHECK_NOTINIT(initialized,word);
+ init();
+ break;
+ case cmd_setRealPrecision:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setRealPrecision(*static_cast<int*>(val));
+ mydatafetcher=DataFetchingObject::create(*static_cast<int*>(val),*this);
+ break;
+ case cmd_setMDLengthUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDLengthUnits(d);
+ break;
+ case cmd_setMDChargeUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDChargeUnits(d);
+ break;
+ case cmd_setMDMassUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDMassUnits(d);
+ break;
+ case cmd_setMDEnergyUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDEnergyUnits(d);
+ break;
+ case cmd_setMDTimeUnits:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.MD2double(val,d);
+ atoms.setMDTimeUnits(d);
+ break;
+ case cmd_setNaturalUnits:
+ // set the boltzman constant for MD in natural units (kb=1)
+ // only needed in LJ codes if the MD is passing temperatures to plumed (so, not yet...)
+ // use as cmd("setNaturalUnits")
+ CHECK_NOTINIT(initialized,word);
+ atoms.setMDNaturalUnits(true);
+ break;
+ case cmd_setNoVirial:
+ CHECK_NOTINIT(initialized,word);
+ novirial=true;
+ break;
+ case cmd_setPlumedDat:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ plumedDat=static_cast<char*>(val);
+ break;
+ case cmd_setMPIComm:
+ CHECK_NOTINIT(initialized,word);
+ comm.Set_comm(val);
+ atoms.setDomainDecomposition(comm);
+ break;
+ case cmd_setMPIFComm:
+ CHECK_NOTINIT(initialized,word);
+ comm.Set_fcomm(val);
+ atoms.setDomainDecomposition(comm);
+ break;
+ case cmd_setMPImultiSimComm:
+ CHECK_NOTINIT(initialized,word);
+ multi_sim_comm.Set_comm(val);
+ break;
+ case cmd_setNatoms:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setNatoms(*static_cast<int*>(val));
+ break;
+ case cmd_setTimestep:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setTimeStep(val);
+ break;
+ /* ADDED WITH API==2 */
+ case cmd_setKbT:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.setKbT(val);
+ break;
+ /* ADDED WITH API==3 */
+ case cmd_setRestart:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ if(*static_cast<int*>(val)!=0) restart=true;
+ break;
+ /* ADDED WITH API==4 */
+ case cmd_doCheckPoint:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ doCheckPoint = false;
+ if(*static_cast<int*>(val)!=0) doCheckPoint = true;
+ break;
+ /* STOP API */
+ case cmd_setMDEngine:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ MDEngine=static_cast<char*>(val);
+ break;
+ case cmd_setLog:
+ CHECK_NOTINIT(initialized,word);
+ log.link(static_cast<FILE*>(val));
+ break;
+ case cmd_setLogFile:
+ CHECK_NOTINIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ log.open(static_cast<char*>(val));
+ break;
+ // other commands that should be used after initialization:
+ case cmd_setStopFlag:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ stopFlag=static_cast<int*>(val);
+ break;
+ case cmd_getExchangesFlag:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.getFlag((*static_cast<int*>(val)));
+ break;
+ case cmd_setExchangesSeed:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.setSeed((*static_cast<int*>(val)));
+ break;
+ case cmd_setNumberOfReplicas:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.setNofR((*static_cast<int*>(val)));
+ break;
+ case cmd_getExchangesList:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ exchangePatterns.getList((static_cast<int*>(val)));
+ break;
+ case cmd_runFinalJobs:
+ CHECK_INIT(initialized,word);
+ runJobsAtEndOfCalculation();
+ break;
+ case cmd_isEnergyNeeded:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ if(atoms.isEnergyNeeded()) *(static_cast<int*>(val))=1;
+ else *(static_cast<int*>(val))=0;
+ break;
+ case cmd_getBias:
+ CHECK_INIT(initialized,word);
+ CHECK_NOTNULL(val,word);
+ atoms.double2MD(getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);
+ break;
+ case cmd_checkAction:
+ CHECK_NOTNULL(val,word);
+ plumed_assert(nw==2);
+ *(static_cast<int*>(val))=(actionRegister().check(words[1]) ? 1:0);
+ break;
+ case cmd_setExtraCV:
+ CHECK_NOTNULL(val,word);
+ plumed_assert(nw==2);
+ atoms.setExtraCV(words[1],val);
+ break;
+ case cmd_setExtraCVForce:
+ CHECK_NOTNULL(val,word);
+ plumed_assert(nw==2);
+ atoms.setExtraCVForce(words[1],val);
+ break;
+ case cmd_GREX:
+ if(!grex) grex.reset(new GREX(*this));
+ plumed_massert(grex,"error allocating grex");
+ {
+ std::string kk=words[1];
+ for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
+ grex->cmd(kk.c_str(),val);
+ }
+ break;
+ case cmd_CLTool:
+ CHECK_NOTINIT(initialized,word);
+ if(!cltool) cltool.reset(new CLToolMain);
+ {
+ std::string kk=words[1];
+ for(unsigned i=2; i<words.size(); i++) kk+=" "+words[i];
+ cltool->cmd(kk.c_str(),val);
+ }
+ break;
+ default:
+ plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
+ break;
}
- break;
- default:
- plumed_merror("cannot interpret cmd(\"" + word + "\"). check plumed developers manual to see the available commands.");
- break;
}
+ stopwatch.pause();
+
+ } catch (Exception &e) {
+ if(log.isOpen()) {
+ log<<"\n\n################################################################################\n\n";
+ log<<e.what();
+ log<<"\n\n################################################################################\n\n";
+ log.flush();
+ }
+ throw;
}
- stopwatch.pause();
}
////////////////////////////////////////////////////////////////////////
@@ -563,12 +568,13 @@ void PlumedMain::readInputWords(const std::vector<std::string> & words) {
Tools::interpretLabel(interpreted);
std::unique_ptr<Action> action(actionRegister().create(ActionOptions(*this,interpreted)));
if(!action) {
- log<<"ERROR\n";
- log<<"I cannot understand line:";
- for(unsigned i=0; i<interpreted.size(); ++i) log<<" "<<interpreted[i];
- log<<"\n";
+ std::string msg;
+ msg ="ERROR\nI cannot understand line:";
+ for(unsigned i=0; i<interpreted.size(); ++i) msg+=" "+interpreted[i];
+ msg+="\nMaybe a missing space or a typo?";
+ log << msg;
log.flush();
- plumed_merror("I cannot understand line " + interpreted[0] + " " + interpreted[1]);
+ plumed_merror(msg);
};
action->checkRead();
actionSet.emplace_back(std::move(action));
@@ -775,17 +781,17 @@ void PlumedMain::update() {
void PlumedMain::load(const std::string& ss) {
if(DLLoader::installed()) {
- string s=ss;
+ std::string s=ss;
size_t n=s.find_last_of(".");
- string extension="";
- string base=s;
+ std::string extension="";
+ std::string base=s;
if(n!=std::string::npos && n<s.length()-1) extension=s.substr(n+1);
if(n!=std::string::npos && n<s.length()) base=s.substr(0,n);
if(extension=="cpp") {
// full path command, including environment setup
// this will work even if plumed is not in the execution path or if it has been
// installed with a name different from "plumed"
- string cmd=config::getEnvCommand()+" \""+config::getPlumedRoot()+"\"/scripts/mklib.sh "+s;
+ std::string cmd=config::getEnvCommand()+" \""+config::getPlumedRoot()+"\"/scripts/mklib.sh "+s;
log<<"Executing: "<<cmd;
if(comm.Get_size()>0) log<<" (only on master node)";
log<<"\n";
diff --git a/src/core/SetupMolInfo.cpp b/src/core/SetupMolInfo.cpp
index 116d66653ab1f667bb0129951480a8e8f96d5c44..878bfb19e9f3087a7604c51f9b86b0ffe6932b3d 100644
--- a/src/core/SetupMolInfo.cpp
+++ b/src/core/SetupMolInfo.cpp
@@ -54,8 +54,7 @@ SetupMolInfo::~SetupMolInfo() {
SetupMolInfo::SetupMolInfo( const ActionOptions&ao ):
Action(ao),
ActionSetup(ao),
- ActionAtomistic(ao),
- pdb_fwd(new(PDB))
+ ActionAtomistic(ao)
{
// Read what is contained in the pdb file
parse("MOLTYPE",mytype);
diff --git a/src/crystallization/PolymerAngles.cpp b/src/crystallization/PolymerAngles.cpp
index 57b1cbfd15734b081fe7518b98e8c77a8ad306cd..b9d97ec24eff662d34238197ecaa614c3898aab4 100644
--- a/src/crystallization/PolymerAngles.cpp
+++ b/src/crystallization/PolymerAngles.cpp
@@ -30,7 +30,7 @@ This CV takes the vectors calculated by a \ref PLANES action as input and comput
of the relative angles, \f$\theta\f$, between the normals of pairs of input vectors:
\f[
-s = \frac{ 3 \cos \theta - 1 }{ 2 }
+s = \frac{ 3 \cos^2 \theta - 1 }{ 2 }
\f]
This average of this quantity over all the vectors in the first coordination sphere around each of the PLANES specified
@@ -94,7 +94,7 @@ double PolymerAngles::computeVectorFunction( const Vector& conn, const std::vect
plumed_assert( (vec1.size()-2)==3 );
double dot = 0; for(unsigned k=0; k<3; ++k) dot += vec1[2+k]*vec2[2+k];
- double ans = 1.5*dot - 0.5; for(unsigned k=0; k<3; ++k) { dvec1[2+k]=1.5*vec2[2+k]; dvec2[2+k]=1.5*vec1[2+k]; }
+ double ans = 1.5*dot*dot - 0.5; for(unsigned k=0; k<3; ++k) { dvec1[2+k]=3*dot*vec2[2+k]; dvec2[2+k]=3*dot*vec1[2+k]; }
return ans;
}
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index 9188c0e3b0a50f2cb026c4e2533dfe336e6c04e5..5583dee4ff7f496f0a0c2c02d3254c9ad1d19597 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -181,7 +181,7 @@ FuncPathMSD::FuncPathMSD(const ActionOptions&ao):
log.printf(" Consistency check completed! Your path cvs look good!\n");
// do some neighbor printout
if(neigh_stride>0. || neigh_size>0) {
- if(neigh_size>getNumberOfArguments()) {
+ if(neigh_size>static_cast<int>(getNumberOfArguments())) {
log.printf(" List size required ( %d ) is too large: resizing to the maximum number of arg required: %d \n",neigh_size,getNumberOfArguments());
neigh_size=getNumberOfArguments();
}
@@ -255,7 +255,7 @@ void FuncPathMSD::prepare() {
// resize the effective list
neighpair.resize(neigh_size);
log.printf(" NEIGH LIST NOW INCLUDE INDEXES: ");
- for(int i=0; i<neigh_size; ++i)log.printf(" %f ",indexmap[neighpair[i].first]); log.printf(" \n");
+ for(int i=0; i<neigh_size; ++i) {log.printf(" %f ",indexmap[neighpair[i].first]);} log.printf(" \n");
} else {
if( int(getStep())%int(neigh_stride/getTimeStep())==0 ) {
log.printf(" Time %f : recalculating full neighlist \n",getStep()*getTimeStep());
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index a0c03f87a9e267a565e2b5ddc0eeacd6a9aa9cac..f142c06e1e6e18e2a80facbaecdddb77949905f0 100644
--- a/src/function/LocalEnsemble.cpp
+++ b/src/function/LocalEnsemble.cpp
@@ -110,7 +110,7 @@ LocalEnsemble::LocalEnsemble(const ActionOptions&ao):
vector<Value*> larg;
if(!parseArgumentList("ARG",i,larg)) break;
for(unsigned j=0; j<larg.size(); j++) arg.push_back(larg[j]);
- if(oldsize!=-1&&oldsize!=larg.size()) error("In LOCALENSEMBLE you should have the same number of arguments for each ARG keyword");
+ if(oldsize!=-1&&oldsize!=static_cast<int>(larg.size())) error("In LOCALENSEMBLE you should have the same number of arguments for each ARG keyword");
oldsize = larg.size();
if(!larg.empty()) {
log.printf(" with arguments %u: ", i);
diff --git a/src/generic/DumpMassCharge.cpp b/src/generic/DumpMassCharge.cpp
index dee8133eca95ef7f68dcd627743ee25315cc7ff5..4134ddf01ecf6a6b38012f62e1a9799e92d20bfa 100644
--- a/src/generic/DumpMassCharge.cpp
+++ b/src/generic/DumpMassCharge.cpp
@@ -128,7 +128,7 @@ DumpMassCharge::DumpMassCharge(const ActionOptions&ao):
parseAtomList("ATOMS",atoms);
if(atoms.size()==0) {
- for(unsigned i=0; i<plumed.getAtoms().getNatoms(); i++) {
+ for(int i=0; i<plumed.getAtoms().getNatoms(); i++) {
atoms.push_back(AtomNumber::index(i));
}
}
@@ -149,7 +149,7 @@ void DumpMassCharge::update() {
of.link(*this);
of.open(file);
- for(int i=0; i<getNumberOfAtoms(); i++) {
+ for(unsigned i=0; i<getNumberOfAtoms(); i++) {
int ii=getAbsoluteIndex(i).index();
of.printField("index",ii);
of.printField("mass",getMass(i));
diff --git a/src/gridtools/HistogramOnGrid.cpp b/src/gridtools/HistogramOnGrid.cpp
index 00a0a3b25cd2f1e49ada3e1389374549b0fad5e0..2644fd4af94e3ce2986d5f79a5b471984e0619c5 100644
--- a/src/gridtools/HistogramOnGrid.cpp
+++ b/src/gridtools/HistogramOnGrid.cpp
@@ -74,13 +74,13 @@ void HistogramOnGrid::setBounds( const std::vector<std::string>& smin, const std
}
}
-KernelFunctions* HistogramOnGrid::getKernelAndNeighbors( std::vector<double>& point, unsigned& num_neigh, std::vector<unsigned>& neighbors ) const {
+std::unique_ptr<KernelFunctions> HistogramOnGrid::getKernelAndNeighbors( std::vector<double>& point, unsigned& num_neigh, std::vector<unsigned>& neighbors ) const {
if( discrete ) {
plumed_assert( getType()=="flat" );
num_neigh=1; for(unsigned i=0; i<dimension; ++i) point[i] += 0.5*dx[i];
neighbors[0] = getIndex( point ); return NULL;
} else if( getType()=="flat" ) {
- KernelFunctions* kernel = new KernelFunctions( point, bandwidths, kerneltype, "DIAGONAL", 1.0 );
+ std::unique_ptr<KernelFunctions> kernel(new KernelFunctions( point, bandwidths, kerneltype, "DIAGONAL", 1.0 ));
kernel->normalize( getVectorOfValues() ); getNeighbors( kernel->getCenter(), nneigh, num_neigh, neighbors );
return kernel;
} else if( getType()=="fibonacci" ) {
@@ -116,7 +116,7 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
// Get the kernel
unsigned num_neigh; std::vector<unsigned> neighbors;
std::vector<double> der( dimension );
- KernelFunctions* kernel=getKernelAndNeighbors( point, num_neigh, neighbors );
+ std::unique_ptr<KernelFunctions> kernel=getKernelAndNeighbors( point, num_neigh, neighbors );
if( !kernel && getType()=="flat" ) {
plumed_dbg_assert( num_neigh==1 ); der.resize(0);
@@ -169,7 +169,6 @@ void HistogramOnGrid::calculate( const unsigned& current, MultiValue& myvals, st
buffer[ bufstart + gridbuf + nder + 1 + kder ] += myvals.getDerivative( 0, kder );
}
}
- if( kernel ) delete kernel;
for(unsigned i=0; i<dimension; ++i) delete vv[i];
}
}
diff --git a/src/gridtools/HistogramOnGrid.h b/src/gridtools/HistogramOnGrid.h
index 44d6988126977c049e531e50575e13d234afc98d..30af6d6332dd2c18dd62a86c759ce03803f9d3d2 100644
--- a/src/gridtools/HistogramOnGrid.h
+++ b/src/gridtools/HistogramOnGrid.h
@@ -23,6 +23,7 @@
#define __PLUMED_gridtools_HistogramOnGrid_h
#include "GridVessel.h"
+#include <memory>
namespace PLMD {
@@ -51,7 +52,7 @@ public:
virtual void accumulate( const unsigned& ipoint, const double& weight, const double& dens, const std::vector<double>& der, std::vector<double>& buffer ) const ;
virtual void accumulateForce( const unsigned& ipoint, const double& weight, const std::vector<double>& der, std::vector<double>& intforce ) const ;
unsigned getNumberOfBufferPoints() const ;
- KernelFunctions* getKernelAndNeighbors( std::vector<double>& point, unsigned& num_neigh, std::vector<unsigned>& neighbors ) const;
+ std::unique_ptr<KernelFunctions> getKernelAndNeighbors( std::vector<double>& point, unsigned& num_neigh, std::vector<unsigned>& neighbors ) const;
std::vector<Value*> getVectorOfValues() const ;
void addOneKernelEachTimeOnly() { addOneKernelAtATime=true; }
virtual void getFinalForces( const std::vector<double>& buffer, std::vector<double>& finalForces );
diff --git a/src/isdb/CS2Backbone.cpp b/src/isdb/CS2Backbone.cpp
index 765d30cb5f78c0bf99169e77c213e31a97b4c19a..798cc3723eef516dcbf72d087e424c962bd21b77 100644
--- a/src/isdb/CS2Backbone.cpp
+++ b/src/isdb/CS2Backbone.cpp
@@ -20,7 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#define cutOffNB 0.70 // buffer distance for neighbour-lists
+#define cutOffNB 0.60 // buffer distance for neighbour-lists
#define cutOffDist 0.50 // cut off distance for non-bonded pairwise forces
#define cutOnDist 0.32 // cut off distance for non-bonded pairwise forces
#define cutOffNB2 cutOffNB*cutOffNB // squared buffer distance for neighbour-lists
@@ -37,8 +37,6 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include "tools/PDB.h"
#include "tools/Torsion.h"
@@ -121,7 +119,7 @@ in NMR driven Metadynamics \cite Granata:2013dk :
\plumedfile
whole: GROUP ATOMS=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1
WHOLEMOLECULES ENTITY0=whole
-cs: CS2BACKBONE ATOMS=1-2612 NRES=176 DATADIR=../data/ TEMPLATE=template.pdb CAMSHIFT NOPBC
+cs: CS2BACKBONE ATOMS=1-2612 DATADIR=../data/ TEMPLATE=template.pdb CAMSHIFT NOPBC
metad: METAD ARG=cs HEIGHT=0.5 SIGMA=0.1 PACE=200 BIASFACTOR=10
PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100
\endplumedfile
@@ -129,7 +127,7 @@ PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100
In this second example the chemical shifts are used as replica-averaged restrained as in \cite Camilloni:2012je \cite Camilloni:2013hs.
\plumedfile
-cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ NRES=13
+cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/
encs: ENSEMBLE ARG=(cs\.hn_.*),(cs\.nh_.*)
stcs: STATS ARG=encs.* SQDEVSUM PARARG=(cs\.exphn_.*),(cs\.expnh_.*)
RESTRAINT ARG=stcs.sqdevsum AT=0 KAPPA=0 SLOPE=24
@@ -141,8 +139,8 @@ PRINT ARG=(cs\.hn_.*),(cs\.nh_.*) FILE=RESTRAINT STRIDE=100
This third example show how to use chemical shifts to calculate a \ref METAINFERENCE score .
\plumedfile
-cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ NRES=13 DOSCORE NDATA=24
-csbias: BIASVALUE ARG=cs
+cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ DOSCORE
+csbias: BIASVALUE ARG=cs.score
PRINT ARG=(cs\.hn_.*),(cs\.nh_.*) FILE=CS.dat STRIDE=1000
PRINT ARG=cs.score FILE=BIAS STRIDE=100
@@ -198,9 +196,7 @@ public:
inline double * CONSTAACURR(const unsigned a_kind, const unsigned at_kind) {return c_aa[a_kind][at_kind];}
inline double * CONSTAANEXT(const unsigned a_kind, const unsigned at_kind) {return c_aa_succ[a_kind][at_kind];}
inline double * CONSTAAPREV(const unsigned a_kind, const unsigned at_kind) {return c_aa_prev[a_kind][at_kind];}
- inline double * CONST_BB2_PREV(const unsigned a_kind, const unsigned at_kind) {return co_bb[a_kind][at_kind];}
- inline double * CONST_BB2_CURR(const unsigned a_kind, const unsigned at_kind) {return co_bb[a_kind][at_kind]+5;}
- inline double * CONST_BB2_NEXT(const unsigned a_kind, const unsigned at_kind) {return co_bb[a_kind][at_kind]+11;}
+ inline double * CONST_BB2(const unsigned a_kind, const unsigned at_kind) {return co_bb[a_kind][at_kind];}
inline double * CONST_SC2(const unsigned a_kind, const unsigned at_kind, unsigned res_type) { return co_sc_[a_kind][at_kind][res_type];}
inline double * CONST_XD(const unsigned a_kind, const unsigned at_kind) { return co_xd[a_kind][at_kind];}
inline double * CO_SPHERE(const unsigned a_kind, const unsigned at_kind, unsigned exp_type) { return co_sphere[a_kind][at_kind][exp_type];}
@@ -211,7 +207,7 @@ public:
void parse(const string &file, const double dscale) {
ifstream in;
in.open(file.c_str());
- if(!in) plumed_merror("Unable to open CS2Backbone DB file " +file);
+ if(!in) plumed_merror("Unable to open DB file: " + file);
unsigned c_kind = 0;
unsigned c_atom = 0;
@@ -366,7 +362,7 @@ public:
if(ok) continue;
if(tok.size()) {
- string str_err = "CS2Backbone DB WARNING: unrecognized token: " + tok[0];
+ string str_err = "DB WARNING: unrecognized token: " + tok[0];
plumed_merror(str_err);
}
}
@@ -399,56 +395,47 @@ private:
};
class CS2Backbone : public MetainferenceBase {
- struct Fragment {
- vector<Value*> comp;
- vector<double> exp_cs;
- unsigned res_type_prev;
- unsigned res_type_curr;
- unsigned res_type_next;
- unsigned res_kind;
- unsigned fd;
+ struct ChemicalShift {
+ double exp_cs; // a reference chemical shifts
+ Value *comp; // a pointer to the component
+ unsigned res_kind; // residue type (STD/GLY/PRO)
+ unsigned atm_kind; // nuclues (HA/CA/CB/CO/NH/HN)
+ unsigned res_type_prev; // previuos residue (ALA/VAL/..)
+ unsigned res_type_curr; // current residue (ALA/VAL/..)
+ unsigned res_type_next; // next residue (ALA/VAL/..)
string res_name;
- vector<int> pos;
- vector<int> prev;
- vector<int> curr;
- vector<int> next;
- vector<int> side_chain;
- vector<int> xd1;
- vector<int> xd2;
- vector<unsigned> box_nb;
- vector<int> phi;
- vector<int> psi;
- vector<int> chi1;
- double t_phi;
- double t_psi;
- double t_chi1;
- vector<Vector> dd0, dd10, dd21, dd2;
-
- Fragment() {
- comp.resize(6);
- exp_cs.resize(6,0);
- res_type_prev = res_type_curr = res_type_next = 0;
- res_kind = 0;
- fd = 0;
- res_name = "";
- pos.resize(6,-1);
- prev.reserve(5);
- curr.reserve(6);
- next.reserve(5);
- side_chain.reserve(20);
- xd1.reserve(27);
- xd2.reserve(27);
- box_nb.reserve(250);
- phi.reserve(4);
- psi.reserve(4);
- chi1.reserve(4);
- t_phi = t_psi = t_chi1 = 0;
- dd0.resize(3);
- dd10.resize(3);
- dd21.resize(3);
- dd2.resize(3);
+ string nucleus;
+ bool has_chi1;
+ unsigned csatoms;
+ unsigned totcsatoms;
+ unsigned res_num;
+ unsigned ipos; // index of the atom for which we are calculating the chemical shifts
+ vector<unsigned> bb;
+ vector<unsigned> side_chain; // atoms for the current sidechain
+ vector<int> xd1; // additional couple of atoms
+ vector<int> xd2; // additional couple of atoms
+ vector<unsigned> box_nb; // non-bonded atoms
+
+ ChemicalShift():
+ exp_cs(0.),
+ comp(NULL),
+ res_kind(0),
+ atm_kind(0),
+ res_type_prev(0),
+ res_type_curr(0),
+ res_type_next(0),
+ res_name(""),
+ nucleus(""),
+ has_chi1(true),
+ csatoms(0),
+ totcsatoms(0),
+ res_num(0),
+ ipos(0)
+ {
+ xd1.reserve(26);
+ xd2.reserve(26);
+ box_nb.reserve(150);
}
-
};
struct RingInfo {
@@ -470,36 +457,30 @@ class CS2Backbone : public MetainferenceBase {
enum aa_t {ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, UNK};
enum atom_t {D_C, D_H, D_N, D_O, D_S, D_C2, D_N2, D_O2};
+ enum sequence_t {Np, CAp, HAp, Cp, Op, Nc, Hc, CAc, HAc, Cc, Oc, Nn, Hn, CAn, HAn, Cn, CBc, CGc};
CS2BackboneDB db;
- vector<vector<Fragment> > atom;
- vector<vector<vector<unsigned> > > index_cs;
+ vector<ChemicalShift> chemicalshifts;
+
vector<RingInfo> ringInfo;
- vector<unsigned> seg_last;
vector<unsigned> type;
vector<unsigned> res_num;
+ unsigned max_cs_atoms;
unsigned box_nupdate;
unsigned box_count;
bool camshift;
bool pbc;
+ bool serial;
- void remove_problematic(const string &res, const string &nucl);
- void read_cs(const string &file, const string &k);
+ void init_cs(const string &file, const string &k, const PDB &pdb);
void update_neighb();
void compute_ring_parameters();
- void compute_dihedrals();
- void init_backbone(const PDB &pdb);
- void init_sidechain(const PDB &pdb);
- void init_xdist(const PDB &pdb);
void init_types(const PDB &pdb);
void init_rings(const PDB &pdb);
aa_t frag2enum(const string &aa);
vector<string> side_chain_atoms(const string &s);
bool isSP2(const string & resType, const string & atomName);
bool is_chi1_cx(const string & frg, const string & atm);
- unsigned frag_segment(const unsigned p);
- unsigned frag_relitive_index(const unsigned p, const unsigned s);
- void debug_report();
void xdist_name_map(string & name);
public:
@@ -517,11 +498,11 @@ void CS2Backbone::registerKeywords( Keywords& keys ) {
useCustomisableComponents(keys);
MetainferenceBase::registerKeywords( keys );
keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
+ keys.addFlag("SERIAL",false,"Perform the calculation in serial - for debug purpose");
keys.add("atoms","ATOMS","The atoms to be included in the calculation, e.g. the whole protein.");
keys.add("compulsory","DATADIR","data/","The folder with the experimental chemical shifts.");
keys.add("compulsory","TEMPLATE","template.pdb","A PDB file of the protein system to initialise ALMOST.");
keys.add("compulsory","NEIGH_FREQ","20","Period in step for neighbour list update.");
- keys.add("compulsory","NRES","Number of residues, corresponding to the number of chemical shifts.");
keys.addFlag("CAMSHIFT",false,"Set to TRUE if you to calculate a single CamShift score.");
keys.addFlag("NOEXP",false,"Set to TRUE if you don't want to have fixed components with the experimetnal values.");
keys.addOutputComponent("ha","default","the calculated Ha hydrogen chemical shifts");
@@ -540,19 +521,23 @@ void CS2Backbone::registerKeywords( Keywords& keys ) {
CS2Backbone::CS2Backbone(const ActionOptions&ao):
PLUMED_METAINF_INIT(ao),
+ max_cs_atoms(0),
camshift(false),
- pbc(true)
+ pbc(true),
+ serial(false)
{
- string stringadb;
- string stringapdb;
+ vector<AtomNumber> used_atoms;
+ parseAtomList("ATOMS",used_atoms);
parseFlag("CAMSHIFT",camshift);
- if(camshift&&getDoScore()) error("It is not possible to use CAMSHIFT together with DOSCORE");
+ if(camshift&&getDoScore()) plumed_merror("It is not possible to use CAMSHIFT and DOSCORE at the same time");
bool nopbc=!pbc;
parseFlag("NOPBC",nopbc);
pbc=!nopbc;
+ parseFlag("SERIAL",serial);
+
bool noexp=false;
parseFlag("NOEXP",noexp);
@@ -566,11 +551,8 @@ CS2Backbone::CS2Backbone(const ActionOptions&ao):
box_nupdate=20;
parse("NEIGH_FREQ", box_nupdate);
- unsigned numResidues;
- parse("NRES", numResidues);
-
- stringadb = stringa_data + string("/camshift.db");
- stringapdb = stringa_data + string("/") + stringa_template;
+ string stringadb = stringa_data + string("/camshift.db");
+ string stringapdb = stringa_data + string("/") + stringa_template;
/* Lenght conversion (parameters are tuned for angstrom) */
double scale=1.;
@@ -578,999 +560,258 @@ CS2Backbone::CS2Backbone(const ActionOptions&ao):
scale = 10.*atoms.getUnits().getLength();
}
- log.printf(" Initialization of the predictor ...\n"); log.flush();
+ log.printf(" Initialization of the predictor ...\n");
db.parse(stringadb,scale);
+
PDB pdb;
- if( !pdb.read(stringapdb,plumed.getAtoms().usingNaturalUnits(),1./scale) ) error("missing input file " + stringapdb);
- init_backbone(pdb);
- init_sidechain(pdb);
- init_xdist(pdb);
- init_types(pdb);
- init_rings(pdb);
-#ifndef NDEBUG
- debug_report();
-#endif
+ if( !pdb.read(stringapdb,plumed.getAtoms().usingNaturalUnits(),1./scale) ) plumed_merror("missing input file " + stringapdb);
+
+ // first of all we build the list of chemical shifts we want to predict
log.printf(" Reading experimental data ...\n"); log.flush();
stringadb = stringa_data + string("/CAshifts.dat");
- log.printf(" Initializing CA shifts %s\n", stringadb.c_str()); log.flush();
- read_cs(stringadb, "CA");
+ log.printf(" Initializing CA shifts %s\n", stringadb.c_str());
+ init_cs(stringadb, "CA", pdb);
stringadb = stringa_data + string("/CBshifts.dat");
- log.printf(" Initializing CB shifts %s\n", stringadb.c_str()); log.flush();
- read_cs(stringadb, "CB");
+ log.printf(" Initializing CB shifts %s\n", stringadb.c_str());
+ init_cs(stringadb, "CB", pdb);
stringadb = stringa_data + string("/Cshifts.dat");
- log.printf(" Initializing C' shifts %s\n", stringadb.c_str()); log.flush();
- read_cs(stringadb, "C");
+ log.printf(" Initializing C' shifts %s\n", stringadb.c_str());
+ init_cs(stringadb, "C", pdb);
stringadb = stringa_data + string("/HAshifts.dat");
- log.printf(" Initializing HA shifts %s\n", stringadb.c_str()); log.flush();
- read_cs(stringadb, "HA");
+ log.printf(" Initializing HA shifts %s\n", stringadb.c_str());
+ init_cs(stringadb, "HA", pdb);
stringadb = stringa_data + string("/Hshifts.dat");
- log.printf(" Initializing H shifts %s\n", stringadb.c_str()); log.flush();
- read_cs(stringadb, "H");
+ log.printf(" Initializing H shifts %s\n", stringadb.c_str());
+ init_cs(stringadb, "H", pdb);
stringadb = stringa_data + string("/Nshifts.dat");
- log.printf(" Initializing N shifts %s\n", stringadb.c_str()); log.flush();
- read_cs(stringadb, "N");
-
- /* this is a workaround for those chemical shifts that can result in too large forces */
- remove_problematic("GLN", "CB");
- remove_problematic("ILE", "CB");
- remove_problematic("PRO", "N");
- remove_problematic("PRO", "H");
- remove_problematic("PRO", "CB");
- remove_problematic("GLY", "HA");
- remove_problematic("GLY", "CB");
- /* this is a workaround for those chemical shifts that are not parameterized */
- remove_problematic("HIE", "HA"); remove_problematic("HIP", "HA"); remove_problematic("HSP", "HA");
- remove_problematic("HIE", "H"); remove_problematic("HIP", "H"); remove_problematic("HSP", "H");
- remove_problematic("HIE", "N"); remove_problematic("HIP", "N"); remove_problematic("HSP", "N");
- remove_problematic("HIE", "CA"); remove_problematic("HIP", "CA"); remove_problematic("HSP", "CA");
- remove_problematic("HIE", "CB"); remove_problematic("HIP", "CB"); remove_problematic("HSP", "CB");
- remove_problematic("HIE", "C"); remove_problematic("HIP", "C"); remove_problematic("HSP", "C");
- remove_problematic("GLH", "HA"); remove_problematic("ASH", "HA"); remove_problematic("HSE", "HA");
- remove_problematic("GLH", "H"); remove_problematic("ASH", "H"); remove_problematic("HSE", "H");
- remove_problematic("GLH", "N"); remove_problematic("ASH", "N"); remove_problematic("HSE", "N");
- remove_problematic("GLH", "CA"); remove_problematic("ASH", "CA"); remove_problematic("HSE", "CA");
- remove_problematic("GLH", "CB"); remove_problematic("ASH", "CB"); remove_problematic("HSE", "CB");
- remove_problematic("GLH", "C"); remove_problematic("ASH", "C"); remove_problematic("HSE", "C");
- remove_problematic("UNK", "HA");
- remove_problematic("UNK", "H");
- remove_problematic("UNK", "N");
- remove_problematic("UNK", "CA");
- remove_problematic("UNK", "CB");
- remove_problematic("UNK", "C");
- remove_problematic("CYS", "HA");
- remove_problematic("CYS", "H");
- remove_problematic("CYS", "N");
- remove_problematic("CYS", "CA");
- remove_problematic("CYS", "CB");
- remove_problematic("CYS", "C");
- remove_problematic("HIS", "HA");
- remove_problematic("HIS", "H");
- remove_problematic("HIS", "N");
- remove_problematic("HIS", "CA");
- remove_problematic("HIS", "CB");
- remove_problematic("HIS", "C");
- /* done */
-
- vector<AtomNumber> atoms;
- parseAtomList("ATOMS",atoms);
+ log.printf(" Initializing N shifts %s\n", stringadb.c_str());
+ init_cs(stringadb, "N", pdb);
+
+ init_types(pdb);
+ init_rings(pdb);
log<<" Bibliography "
<<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)");
if(camshift) log<<plumed.cite("Granata D, Camilloni C, Vendruscolo M, Laio A, Proc. Natl. Acad. Sci. USA 110, 6817 (2013)");
else log<<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)");
+ log<<plumed.cite("Bonomi M, Camilloni C, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
- const string str_cs[] = {"ha_","hn_","nh_","ca_","cb_","co_"};
- unsigned index=0;
if(camshift) {
noexp = true;
addValueWithDerivatives();
setNotPeriodic();
} else {
- if(getDoScore()) {
- index_cs.resize(atom.size(), vector<vector<unsigned> >());
- for(unsigned i=0; i<atom.size(); i++) {
- index_cs[i].resize(atom[i].size(), vector<unsigned>(6));
- }
- }
- unsigned l=0;
- for(unsigned i=0; i<atom.size(); i++) {
- for(unsigned a=0; a<atom[i].size(); a++) {
- unsigned res=index+a;
- std::string num; Tools::convert(res,num);
- for(unsigned at_kind=0; at_kind<6; at_kind++) {
- if(atom[i][a].exp_cs[at_kind]!=0) {
- if(getDoScore()) {
- addComponent(str_cs[at_kind]+num);
- componentIsNotPeriodic(str_cs[at_kind]+num);
- atom[i][a].comp[at_kind] = getPntrToComponent(str_cs[at_kind]+num);
- index_cs[i][a][at_kind]=l;
- setParameter(atom[i][a].exp_cs[at_kind]);
- l++;
- } else {
- addComponentWithDerivatives(str_cs[at_kind]+num);
- componentIsNotPeriodic(str_cs[at_kind]+num);
- atom[i][a].comp[at_kind] = getPntrToComponent(str_cs[at_kind]+num);
- }
- }
- }
+ for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
+ std::string num; Tools::convert(chemicalshifts[cs].res_num,num);
+ if(getDoScore()) {
+ addComponent(chemicalshifts[cs].nucleus+num);
+ componentIsNotPeriodic(chemicalshifts[cs].nucleus+num);
+ chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+num);
+ setParameter(chemicalshifts[cs].exp_cs);
+ } else {
+ addComponentWithDerivatives(chemicalshifts[cs].nucleus+num);
+ componentIsNotPeriodic(chemicalshifts[cs].nucleus+num);
+ chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+num);
}
- index += atom[i].size();
}
- if(getDoScore()) Initialise(l);
+ if(getDoScore()) Initialise(chemicalshifts.size());
}
if(!noexp) {
- index = 0;
- for(unsigned i=0; i<atom.size(); i++) {
- for(unsigned a=0; a<atom[i].size(); a++) {
- unsigned res=index+a;
- std::string num; Tools::convert(res,num);
- for(unsigned at_kind=0; at_kind<6; at_kind++) {
- if(atom[i][a].exp_cs[at_kind]!=0) {
- addComponent("exp"+str_cs[at_kind]+num);
- componentIsNotPeriodic("exp"+str_cs[at_kind]+num);
- Value* comp=getPntrToComponent("exp"+str_cs[at_kind]+num);
- comp->set(atom[i][a].exp_cs[at_kind]);
- }
- }
- }
- index += atom[i].size();
+ for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
+ std::string num; Tools::convert(chemicalshifts[cs].res_num,num);
+ addComponent("exp"+chemicalshifts[cs].nucleus+num);
+ componentIsNotPeriodic("exp"+chemicalshifts[cs].nucleus+num);
+ Value* comp=getPntrToComponent("exp"+chemicalshifts[cs].nucleus+num);
+ comp->set(chemicalshifts[cs].exp_cs);
}
}
- /* temporary check, the idea is that I can remove NRES completely */
- index=0;
- for(unsigned i=0; i<atom.size(); i++) {
- index += atom[i].size();
- }
- if(index!=numResidues) error("NRES and the number of residues in the PDB do not match!");
-
- requestAtoms(atoms);
+ requestAtoms(used_atoms);
setDerivatives();
checkRead();
}
-void CS2Backbone::remove_problematic(const string &res, const string &nucl) {
- unsigned n;
- if(nucl=="HA") n=0;
- else if(nucl=="H") n=1;
- else if(nucl=="N") n=2;
- else if(nucl=="CA")n=3;
- else if(nucl=="CB")n=4;
- else if(nucl=="C") n=5;
- else return;
-
- for(unsigned i=0; i<atom.size(); i++) {
- for(unsigned a=0; a<atom[i].size(); a++) {
- if(atom[i][a].res_name.c_str()==res) {
- atom[i][a].exp_cs[n] = 0;
- }
- }
- }
-}
+void CS2Backbone::init_cs(const string &file, const string &nucl, const PDB &pdb) {
+ // number of chains
+ vector<string> chains;
+ pdb.getChainNames( chains );
+ unsigned ichain=0;
-void CS2Backbone::read_cs(const string &file, const string &nucl) {
ifstream in;
in.open(file.c_str());
- if(!in) error("CS2Backbone: Unable to open " + file);
+ if(!in) plumed_merror("Unable to open " + file);
istream_iterator<string> iter(in), end;
+ unsigned begin=0;
- unsigned n;
- if(nucl=="HA") n=0;
- else if(nucl=="H") n=1;
- else if(nucl=="N") n=2;
- else if(nucl=="CA")n=3;
- else if(nucl=="CB")n=4;
- else if(nucl=="C") n=5;
- else return;
-
- int oldseg = -1;
- int oldp = -1;
while(iter!=end) {
- string tok;
- tok = *iter; ++iter;
- if(tok[0]=='#') { ++iter; continue;}
- unsigned p = atoi(tok.c_str());
- p = p - 1;
- const unsigned seg = frag_segment(p);
- p = frag_relitive_index(p,seg);
- if(oldp==-1) oldp=p;
- if(oldseg==-1) oldseg=seg;
- if(p<oldp&&seg==oldseg) {
- string errmsg = "Error while reading " + file + "! The same residue number has been used twice!";
- error(errmsg);
+ string tok = *iter;
+ ++iter;
+ if(tok[0]=='#') {
+ ++iter;
+ if(begin==1) {
+ begin=0;
+ ichain++;
+ } else begin=1;
+ continue;
}
- tok = *iter; ++iter;
+ int resnum = atoi(tok.c_str());
+ tok = *iter;
+ ++iter;
double cs = atof(tok.c_str());
- if(atom[seg][p].pos[n]<=0) cs=0;
- else atom[seg][p].exp_cs[n] = cs;
- oldseg = seg;
- oldp = p;
- }
- in.close();
-}
+ if(cs==0) continue;
-void CS2Backbone::calculate()
-{
- if(pbc) makeWhole();
- if(getExchangeStep()) box_count=0;
- if(box_count==0) update_neighb();
-
- compute_ring_parameters();
- compute_dihedrals();
-
- double score = 0.;
-
- vector<double> camshift_sigma2(6);
- camshift_sigma2[0] = 0.08; // HA
- camshift_sigma2[1] = 0.30; // HN
- camshift_sigma2[2] = 9.00; // NH
- camshift_sigma2[3] = 1.30; // CA
- camshift_sigma2[4] = 1.56; // CB
- camshift_sigma2[5] = 1.70; // CO
-
- const unsigned chainsize = atom.size();
- const unsigned atleastned = 72+ringInfo.size()*6;
-
- vector<vector<unsigned> > all_list;
- vector<vector<Vector> > all_ff;
- if(getDoScore()) {
- all_list.resize(getNarg(), vector<unsigned>());
- all_ff.resize(getNarg(), vector<Vector>());
- }
-
- // CYCLE OVER MULTIPLE CHAINS
- #pragma omp parallel num_threads(OpenMP::getNumThreads())
- for(unsigned s=0; s<chainsize; s++) {
- const unsigned psize = atom[s].size();
- vector<Vector> omp_deriv;
- if(camshift) omp_deriv.resize(getNumberOfAtoms(), Vector(0,0,0));
- #pragma omp for reduction(+:score)
- // SKIP FIRST AND LAST RESIDUE OF EACH CHAIN
- for(unsigned a=1; a<psize-1; a++) {
-
- const Fragment *myfrag = &atom[s][a];
- const unsigned aa_kind = myfrag->res_kind;
- const unsigned needed_atoms = atleastned+myfrag->box_nb.size();
-
- /* Extra Distances are the same for each residue */
- const unsigned xdsize=myfrag->xd1.size();
- vector<Vector> ext_distances(xdsize);
- vector<double> ext_d(xdsize);
- for(unsigned q=0; q<xdsize; q++) {
- if(myfrag->xd1[q]==-1||myfrag->xd2[q]==-1) continue;
- const Vector distance = delta(getPosition(myfrag->xd1[q]),getPosition(myfrag->xd2[q]));
- ext_d[q] = distance.modulo();
- ext_distances[q] = distance/ext_d[q];
- }
-
- // CYCLE OVER THE SIX BACKBONE CHEMICAL SHIFTS
- for(unsigned at_kind=0; at_kind<6; at_kind++) {
- if(atom[s][a].exp_cs[at_kind]!=0) {
- // Common constant and AATYPE
- const double * CONSTAACURR = db.CONSTAACURR(aa_kind,at_kind);
- const double * CONSTAANEXT = db.CONSTAANEXT(aa_kind,at_kind);
- const double * CONSTAAPREV = db.CONSTAAPREV(aa_kind,at_kind);
-
- double cs = CONSTAACURR[myfrag->res_type_curr] +
- CONSTAANEXT[myfrag->res_type_next] +
- CONSTAAPREV[myfrag->res_type_prev];
- // this is the atom for which we are calculating the chemical shift
- const unsigned ipos = myfrag->pos[at_kind];
-
- vector<unsigned> list;
- list.reserve(needed_atoms);
- list.push_back(ipos);
- vector<Vector> ff;
- ff.reserve(needed_atoms);
- ff.push_back(Vector(0,0,0));
-
-
- //PREV
- const double * CONST_BB2_PREV = db.CONST_BB2_PREV(aa_kind,at_kind);
- const unsigned presize = myfrag->prev.size();
- for(unsigned q=0; q<presize; q++) {
- const double cb2pq = CONST_BB2_PREV[q];
- if(cb2pq==0.) continue;
- const unsigned jpos = myfrag->prev[q];
- list.push_back(jpos);
- const Vector distance = delta(getPosition(jpos),getPosition(ipos));
- const double d = distance.modulo();
- const double fact = cb2pq/d;
-
- cs += cb2pq*d;
- const Vector der = fact*distance;
- ff[0] += der;
- ff.push_back(-der);
- }
-
- //CURR
- const double * CONST_BB2_CURR = db.CONST_BB2_CURR(aa_kind,at_kind);
- const unsigned cursize = myfrag->curr.size();
- for(unsigned q=0; q<cursize; q++) {
- const double cb2cq = CONST_BB2_CURR[q];
- if(cb2cq==0.) continue;
- const unsigned jpos = myfrag->curr[q];
- if(ipos==jpos) continue;
- list.push_back(jpos);
- const Vector distance = delta(getPosition(jpos),getPosition(ipos));
- const double d = distance.modulo();
- const double fact = cb2cq/d;
-
- cs += cb2cq*d;
- const Vector der = fact*distance;
- ff[0] += der;
- ff.push_back(-der);
- }
-
- //NEXT
- const double * CONST_BB2_NEXT = db.CONST_BB2_NEXT(aa_kind,at_kind);
- const unsigned nexsize = myfrag->next.size();
- for(unsigned q=0; q<nexsize; q++) {
- const double cb2nq = CONST_BB2_NEXT[q];
- if(cb2nq==0.) continue;
- const unsigned jpos = myfrag->next[q];
- list.push_back(jpos);
- const Vector distance = delta(getPosition(jpos),getPosition(ipos));
- const double d = distance.modulo();
- const double fact = cb2nq/d;
-
- cs += cb2nq*d;
- const Vector der = fact*distance;
- ff[0] += der;
- ff.push_back(-der);
- }
-
- //SIDE CHAIN
- const double * CONST_SC2 = db.CONST_SC2(aa_kind,at_kind,myfrag->res_type_curr);
- const unsigned sidsize = myfrag->side_chain.size();
- for(unsigned q=0; q<sidsize; q++) {
- const double cs2q = CONST_SC2[q];
- if(cs2q==0.) continue;
- const unsigned jpos = myfrag->side_chain[q];
- if(ipos==jpos) continue;
- list.push_back(jpos);
- const Vector distance = delta(getPosition(jpos),getPosition(ipos));
- const double d = distance.modulo();
- const double fact = cs2q/d;
-
- cs += cs2q*d;
- const Vector der = fact*distance;
- ff[0] += der;
- ff.push_back(-der);
- }
-
- //EXTRA DIST
- const double * CONST_XD = db.CONST_XD(aa_kind,at_kind);
- for(unsigned q=0; q<xdsize; q++) {
- const double cxdq = CONST_XD[q];
- if(cxdq==0.) continue;
- if(myfrag->xd1[q]==-1||myfrag->xd2[q]==-1) continue;
- list.push_back(myfrag->xd2[q]);
- list.push_back(myfrag->xd1[q]);
- cs += cxdq*ext_d[q];
- const Vector der = cxdq*ext_distances[q];
- ff.push_back( der);
- ff.push_back(-der);
- }
-
- //NON BOND
- {
- const double * CONST_CO_SPHERE3 = db.CO_SPHERE(aa_kind,at_kind,0);
- const double * CONST_CO_SPHERE = db.CO_SPHERE(aa_kind,at_kind,1);
- const unsigned boxsize = myfrag->box_nb.size();
- for(unsigned bat=0; bat<boxsize; bat++) {
- const unsigned jpos = myfrag->box_nb[bat];
- const Vector distance = delta(getPosition(jpos),getPosition(ipos));
- const double d2 = distance.modulo2();
-
- if(d2<cutOffDist2) {
- double factor1 = sqrt(d2);
- double dfactor1 = 1./factor1;
- double factor3 = dfactor1*dfactor1*dfactor1;
- double dfactor3 = -3.*factor3*dfactor1*dfactor1;
-
- if(d2>cutOnDist2) {
- const double af = cutOffDist2 - d2;
- const double bf = cutOffDist2 - 3.*cutOnDist2 + 2.*d2;
- const double cf = invswitch*af;
- const double df = cf*af*bf;
- factor1 *= df;
- factor3 *= df;
-
- const double d4 = d2*d2;
- const double af1 = 15.*cutOnDist2*d2;
- const double bf1 = -14.*d4;
- const double cf1 = -3.*cutOffDist2*cutOnDist2 + cutOffDist2*d2;
- const double df1 = af1+bf1+cf1;
- dfactor1 *= cf*(cutOffDist4+df1);
-
- const double af3 = +2.*cutOffDist2*cutOnDist2;
- const double bf3 = d2*(cutOffDist2+cutOnDist2);
- const double cf3 = -2.*d4;
- const double df3 = (af3+bf3+cf3)*d2;
- dfactor3 *= invswitch*(cutMixed+df3);
- }
-
- const unsigned t = type[jpos];
- cs += factor1*CONST_CO_SPHERE[t] + factor3*CONST_CO_SPHERE3[t] ;
- const double fact = dfactor1*CONST_CO_SPHERE[t]+dfactor3*CONST_CO_SPHERE3[t];
- const Vector der = fact*distance;
-
- list.push_back(jpos);
- ff[0] += der;
- ff.push_back(-der);
- }
- }
- }
- //END NON BOND
-
- //RINGS
- {
- const double *rc = db.CO_RING(aa_kind,at_kind);
- const unsigned rsize = ringInfo.size();
- for(unsigned i=0; i<rsize; i++) {
- // compute angle from ring middle point to current atom position
- // get distance vector from query atom to ring center and normal vector to ring plane
- const Vector n = ringInfo[i].normVect;
- const double nL = ringInfo[i].lengthNV;
- const double inL2 = ringInfo[i].lengthN2;
-
- const Vector d = delta(ringInfo[i].position, getPosition(ipos));
- const double dL2 = d.modulo2();
- double dL = sqrt(dL2);
- const double idL3 = 1./(dL2*dL);
-
- const double dn = dotProduct(d,n);
- const double dn2 = dn*dn;
- const double dLnL = dL*nL;
- const double dL_nL = dL/nL;
-
- const double ang2 = dn2*inL2/dL2;
- const double u = 1.-3.*ang2;
- const double cc = rc[ringInfo[i].rtype];
-
- cs += cc*u*idL3;
-
- const double fUU = -6*dn*inL2;
- const double fUQ = fUU/dL;
- const Vector gradUQ = fUQ*(dL2*n - dn*d);
- const Vector gradVQ = (3*dL*u)*d;
-
- const double fact = cc*idL3*idL3;
- ff[0] += fact*(gradUQ - gradVQ);
-
- const double fU = fUU/nL;
- double OneOverN = 1./6.;
- if(ringInfo[i].numAtoms==5) OneOverN=1./3.;
- const Vector factor2 = OneOverN*n;
- const Vector factor4 = (OneOverN/dL_nL)*d;
-
- const Vector gradV = -OneOverN*gradVQ;
-
- if(ringInfo[i].numAtoms==6) {
- // update forces on ring atoms
- for(unsigned at=0; at<6; at++) {
- const Vector ab = crossProduct(d,ringInfo[i].g[at]);
- const Vector c = crossProduct(n,ringInfo[i].g[at]);
- const Vector factor3 = 0.5*dL_nL*c;
- const Vector factor1 = 0.5*ab;
- const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
- ff.push_back(fact*(gradU - gradV));
- list.push_back(ringInfo[i].atom[at]);
- }
- } else {
- for(unsigned at=0; at<3; at++) {
- const Vector ab = crossProduct(d,ringInfo[i].g[at]);
- const Vector c = crossProduct(n,ringInfo[i].g[at]);
- const Vector factor3 = dL_nL*c;
- const Vector factor1 = ab;
- const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
- ff.push_back(fact*(gradU - gradV));
- }
- list.push_back(ringInfo[i].atom[0]);
- list.push_back(ringInfo[i].atom[2]);
- list.push_back(ringInfo[i].atom[3]);
- }
- }
- }
- //END OF RINGS
-
- //DIHEDRAL ANGLES
- {
- const double *CO_DA = db.CO_DA(aa_kind,at_kind);
- if(myfrag->phi.size()==4) {
- const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,0);
- const double val1 = 3.*myfrag->t_phi+PARS_DA[3];
- const double val2 = myfrag->t_phi+PARS_DA[4];
- cs += CO_DA[0]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
- const double fact = -CO_DA[0]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
-
- ff.push_back(fact*myfrag->dd0[0]);
- ff.push_back(fact*myfrag->dd10[0]);
- ff.push_back(fact*myfrag->dd21[0]);
- ff.push_back(-fact*myfrag->dd2[0]);
- list.push_back(myfrag->phi[0]);
- list.push_back(myfrag->phi[1]);
- list.push_back(myfrag->phi[2]);
- list.push_back(myfrag->phi[3]);
- }
-
- if(myfrag->psi.size()==4) {
- const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,1);
- const double val1 = 3.*myfrag->t_psi+PARS_DA[3];
- const double val2 = myfrag->t_psi+PARS_DA[4];
- cs += CO_DA[1]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
- const double fact = -CO_DA[1]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
-
- ff.push_back(fact*myfrag->dd0[1]);
- ff.push_back(fact*myfrag->dd10[1]);
- ff.push_back(fact*myfrag->dd21[1]);
- ff.push_back(-fact*myfrag->dd2[1]);
- list.push_back(myfrag->psi[0]);
- list.push_back(myfrag->psi[1]);
- list.push_back(myfrag->psi[2]);
- list.push_back(myfrag->psi[3]);
- }
-
- //Chi
- if(myfrag->chi1.size()==4) {
- const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,2);
- const double val1 = 3.*myfrag->t_chi1+PARS_DA[3];
- const double val2 = myfrag->t_chi1+PARS_DA[4];
- cs += CO_DA[2]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
- const double fact = -CO_DA[2]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
-
- ff.push_back(fact*myfrag->dd0[2]);
- ff.push_back(fact*myfrag->dd10[2]);
- ff.push_back(fact*myfrag->dd21[2]);
- ff.push_back(-fact*myfrag->dd2[2]);
- list.push_back(myfrag->chi1[0]);
- list.push_back(myfrag->chi1[1]);
- list.push_back(myfrag->chi1[2]);
- list.push_back(myfrag->chi1[3]);
- }
- }
- //END OF DIHE
-
- if(getDoScore()) {
- setCalcData(index_cs[s][a][at_kind], cs);
- all_list[index_cs[s][a][at_kind]] = list;
- all_ff[index_cs[s][a][at_kind]] = ff;
- Value *comp = atom[s][a].comp[at_kind];
- comp->set(cs);
- } else {
- if(camshift) {
- score += (cs - atom[s][a].exp_cs[at_kind])*(cs - atom[s][a].exp_cs[at_kind])/camshift_sigma2[at_kind];
- double fact = 2.0*(cs - atom[s][a].exp_cs[at_kind])/camshift_sigma2[at_kind];
- for(unsigned i=0; i<list.size(); i++) omp_deriv[list[i]] += fact*ff[i];
- } else {
- Value *comp = atom[s][a].comp[at_kind];
- comp->set(cs);
- Tensor virial;
- for(unsigned i=0; i<list.size(); i++) {
- setAtomsDerivatives(comp,list[i],ff[i]);
- virial-=Tensor(getPosition(list[i]),ff[i]);
- }
- setBoxDerivatives(comp,virial);
- }
- }
- }
- }
- }
- #pragma omp critical
- if(camshift) for(int i=0; i<getPositions().size(); i++) setAtomsDerivatives(getPntrToValue(),i,omp_deriv[i]);
- }
-
- if(getDoScore()) {
- /* Metainference */
- double score = getScore();
- setScore(score);
-
- /* calculate final derivatives */
- Value* val=getPntrToComponent("score");
-
- Tensor virial;
-
- for(unsigned i=0; i<all_list.size(); i++) {
- const double fact = getMetaDer(i);
- for(unsigned j=0; j<all_list[i].size(); j++) {
- setAtomsDerivatives(val, all_list[i][j], all_ff[i][j]*fact);
- virial-=Tensor(getPosition(all_list[i][j]), all_ff[i][j]*fact);
- }
- }
- setBoxDerivatives(val,virial);
- }
-
- // in the case of camshift we calculate the virial at the end
- if(camshift) {
- Tensor virial;
- unsigned nat=getNumberOfAtoms();
- Value* val=getPntrToValue();
- for(unsigned i=0; i<nat; i++) virial-=Tensor(getPosition(i),
- Vector(val->getDerivative(3*i+0),
- val->getDerivative(3*i+1),
- val->getDerivative(3*i+2)));
- setBoxDerivatives(val,virial);
- setValue(score);
- }
-
- ++box_count;
- if(box_count == box_nupdate) box_count = 0;
-}
-
-void CS2Backbone::update_neighb() {
- const unsigned chainsize = atom.size();
- for(unsigned s=0; s<chainsize; s++) {
- const unsigned psize = atom[s].size();
- #pragma omp parallel for num_threads(OpenMP::getNumThreads())
- for(unsigned a=1; a<psize-1; a++) {
- const unsigned boxsize = getNumberOfAtoms();
- atom[s][a].box_nb.clear();
- atom[s][a].box_nb.reserve(300);
- const unsigned res_curr = res_num[atom[s][a].pos[0]];
- for(unsigned bat=0; bat<boxsize; bat++) {
- const unsigned res_dist = abs(static_cast<int>(res_curr-res_num[bat]));
- if(res_dist<2) continue;
- for(unsigned at_kind=0; at_kind<6; at_kind++) {
- if(atom[s][a].exp_cs[at_kind]==0.) continue;
- const unsigned ipos = atom[s][a].pos[at_kind];
- const Vector distance = delta(getPosition(bat),getPosition(ipos));
- const double d2=distance.modulo2();
- if(d2<cutOffNB2) {
- atom[s][a].box_nb.push_back(bat);
- break;
- }
- }
- }
+ unsigned fres, lres;
+ string errmsg;
+ pdb.getResidueRange(chains[ichain], fres, lres, errmsg);
+ if(resnum==fres||resnum==lres) plumed_merror("First and Last residue of each chain should be annotated as # in " + file + " Remember that residue numbers should match");
+
+ // check in the PDB for the chain/residue/atom and enable the chemical shift
+ string RES = pdb.getResidueName(resnum, chains[ichain]);
+ if(RES=="HIE"||RES=="HIP"||RES=="HIS"||RES=="HSP"||RES=="HSE"||RES=="CYS"||RES=="GLH"||RES=="ASH"||RES=="UNK") continue;
+ if(RES=="GLN"&&nucl=="CB") continue;
+ if(RES=="ILE"&&nucl=="CB") continue;
+ if(RES=="PRO"&&nucl=="N") continue;
+ if(RES=="PRO"&&nucl=="H") continue;
+ if(RES=="PRO"&&nucl=="CB") continue;
+ if(RES=="GLY"&&nucl=="HA") continue;
+ if(RES=="GLY"&&nucl=="CB") continue;
+
+ ChemicalShift tmp_cs;
+
+ tmp_cs.exp_cs = cs;
+ if(nucl=="CA") tmp_cs.nucleus = "ca_";
+ else if(nucl=="CB") tmp_cs.nucleus = "cb_";
+ else if(nucl=="C") tmp_cs.nucleus = "co_";
+ else if(nucl=="HA") tmp_cs.nucleus = "ha_";
+ else if(nucl=="H") tmp_cs.nucleus = "hn_";
+ else if(nucl=="N") tmp_cs.nucleus = "nh_";
+ tmp_cs.res_num = resnum;
+ tmp_cs.res_type_curr = frag2enum(RES);
+ tmp_cs.res_type_prev = frag2enum(pdb.getResidueName(resnum-1, chains[ichain]));
+ tmp_cs.res_type_next = frag2enum(pdb.getResidueName(resnum+1, chains[ichain]));
+ tmp_cs.res_name = RES;
+ tmp_cs.res_kind = db.kind(RES);
+ tmp_cs.atm_kind = db.atom_kind(nucl);
+ if(RES!="ALA"&&RES!="GLY") {tmp_cs.bb.resize(18); tmp_cs.has_chi1=true;}
+ else {tmp_cs.bb.resize(16); tmp_cs.has_chi1=false;}
+
+ vector<AtomNumber> res_atoms = pdb.getAtomsInResidue(resnum, chains[ichain]);
+ // find the position of the nucleus and of the other backbone atoms as well as for phi/psi/chi
+ for(unsigned a=0; a<res_atoms.size(); a++) {
+ string AN = pdb.getAtomName(res_atoms[a]);
+ if(nucl=="HA"&&(AN=="HA"||AN=="HA1"||AN=="HA3")) tmp_cs.ipos = res_atoms[a].index();
+ else if(nucl=="H"&&(AN=="H"||AN=="HN")) tmp_cs.ipos = res_atoms[a].index();
+ else if(nucl=="N"&&AN=="N") tmp_cs.ipos = res_atoms[a].index();
+ else if(nucl=="CA"&&AN=="CA") tmp_cs.ipos = res_atoms[a].index();
+ else if(nucl=="CB"&&AN=="CB") tmp_cs.ipos = res_atoms[a].index();
+ else if(nucl=="C"&&AN=="C" ) tmp_cs.ipos = res_atoms[a].index();
}
- }
-}
-
-void CS2Backbone::compute_ring_parameters() {
- for(unsigned i=0; i<ringInfo.size(); i++) {
- const unsigned size = ringInfo[i].numAtoms;
- if(size==6) {
- ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[4]),getPosition(ringInfo[i].atom[2]));
- ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[5]),getPosition(ringInfo[i].atom[3]));
- ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[4]));
- ringInfo[i].g[3] = delta(getPosition(ringInfo[i].atom[1]),getPosition(ringInfo[i].atom[5]));
- ringInfo[i].g[4] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
- ringInfo[i].g[5] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[1]));
- vector<Vector> a(size);
- a[0] = getPosition(ringInfo[i].atom[0]);
- // ring center
- Vector midP = a[0];
- for(unsigned j=1; j<size; j++) {
- a[j] = getPosition(ringInfo[i].atom[j]);
- midP += a[j];
- }
- midP /= (double) size;
- ringInfo[i].position = midP;
- // compute normal vector to plane containing first three atoms in array
- ringInfo[i].n1 = crossProduct(delta(a[0],a[4]), delta(a[0],a[2]));
- // compute normal vector to plane containing last three atoms in array
- // NB: third atom of five-membered ring used for both computations above
- ringInfo[i].n2 = crossProduct(delta(a[3],a[1]), delta(a[3],a[5]));
- // ring plane normal vector is average of n1 and n2
- ringInfo[i].normVect = 0.5*(ringInfo[i].n1 + ringInfo[i].n2);
- } else {
- ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[2]));
- ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[3]));
- ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
- vector<Vector> a(size);
- for(unsigned j=0; j<size; j++) {
- a[j] = getPosition(ringInfo[i].atom[j]);
- }
- // ring center
- Vector midP = (a[0]+a[2]+a[3])/3.;
- ringInfo[i].position = midP;
- // compute normal vector to plane containing first three atoms in array
- ringInfo[i].n1 = crossProduct(delta(a[0],a[3]), delta(a[0],a[2]));
- // ring plane normal vector is average of n1 and n2
- ringInfo[i].normVect = ringInfo[i].n1;
+ vector<AtomNumber> prev_res_atoms = pdb.getAtomsInResidue(resnum-1, chains[ichain]);
+ // find the position of the previous residues backbone atoms
+ for(unsigned a=0; a<prev_res_atoms.size(); a++) {
+ string AN = pdb.getAtomName(prev_res_atoms[a]);
+ if(AN=="N") { tmp_cs.bb[Np] = prev_res_atoms[a].index(); }
+ else if(AN=="CA") { tmp_cs.bb[CAp] = prev_res_atoms[a].index(); }
+ else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAp] = prev_res_atoms[a].index(); }
+ else if(AN=="C" ) { tmp_cs.bb[Cp] = prev_res_atoms[a].index(); }
+ else if(AN=="O" ) { tmp_cs.bb[Op] = prev_res_atoms[a].index(); }
}
- // calculate squared length and length of normal vector
- ringInfo[i].lengthN2 = 1./ringInfo[i].normVect.modulo2();
- ringInfo[i].lengthNV = 1./sqrt(ringInfo[i].lengthN2);
- }
-}
-void CS2Backbone::compute_dihedrals() {
- const unsigned chainsize = atom.size();
- for(unsigned s=0; s<chainsize; s++) {
- const unsigned psize = atom[s].size();
- #pragma omp parallel for num_threads(OpenMP::getNumThreads())
- for(unsigned a=1; a<psize-1; a++) {
- const Fragment *myfrag = &atom[s][a];
- if(myfrag->phi.size()==4) {
- const Vector d0 = delta(getPosition(myfrag->phi[1]), getPosition(myfrag->phi[0]));
- const Vector d1 = delta(getPosition(myfrag->phi[2]), getPosition(myfrag->phi[1]));
- const Vector d2 = delta(getPosition(myfrag->phi[3]), getPosition(myfrag->phi[2]));
- Torsion t;
- Vector dd0, dd1, dd2;
- atom[s][a].t_phi = t.compute(d0,d1,d2,dd0,dd1,dd2);
- atom[s][a].dd0[0] = dd0;
- atom[s][a].dd10[0] = dd1-dd0;
- atom[s][a].dd21[0] = dd2-dd1;
- atom[s][a].dd2[0] = dd2;
- }
- if(myfrag->psi.size()==4) {
- const Vector d0 = delta(getPosition(myfrag->psi[1]), getPosition(myfrag->psi[0]));
- const Vector d1 = delta(getPosition(myfrag->psi[2]), getPosition(myfrag->psi[1]));
- const Vector d2 = delta(getPosition(myfrag->psi[3]), getPosition(myfrag->psi[2]));
- Torsion t;
- Vector dd0, dd1, dd2;
- atom[s][a].t_psi = t.compute(d0,d1,d2,dd0,dd1,dd2);
- atom[s][a].dd0[1] = dd0;
- atom[s][a].dd10[1] = dd1-dd0;
- atom[s][a].dd21[1] = dd2-dd1;
- atom[s][a].dd2[1] = dd2;
- }
- if(myfrag->chi1.size()==4) {
- const Vector d0 = delta(getPosition(myfrag->chi1[1]), getPosition(myfrag->chi1[0]));
- const Vector d1 = delta(getPosition(myfrag->chi1[2]), getPosition(myfrag->chi1[1]));
- const Vector d2 = delta(getPosition(myfrag->chi1[3]), getPosition(myfrag->chi1[2]));
- Torsion t;
- Vector dd0, dd1, dd2;
- atom[s][a].t_chi1 = t.compute(d0,d1,d2,dd0,dd1,dd2);
- atom[s][a].dd0[2] = dd0;
- atom[s][a].dd10[2] = dd1-dd0;
- atom[s][a].dd21[2] = dd2-dd1;
- atom[s][a].dd2[2] = dd2;
+ for(unsigned a=0; a<res_atoms.size(); a++) {
+ string AN = pdb.getAtomName(res_atoms[a]);
+ if(AN=="N") { tmp_cs.bb[Nc] = res_atoms[a].index(); }
+ else if(AN=="H" ||AN=="HN"||(AN=="CD"&&RES=="PRO")) { tmp_cs.bb[Hc] = res_atoms[a].index(); }
+ else if(AN=="CA") { tmp_cs.bb[CAc] = res_atoms[a].index(); }
+ else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAc] = res_atoms[a].index(); }
+ else if(AN=="C" ) { tmp_cs.bb[Cc] = res_atoms[a].index(); }
+ else if(AN=="O" ) { tmp_cs.bb[Oc] = res_atoms[a].index(); }
+
+ if(RES!="ALA"&&RES!="GLY") {
+ if(AN=="CB") tmp_cs.bb[CBc] = res_atoms[a].index();
+ if(is_chi1_cx(RES,AN)) tmp_cs.bb[CGc] = res_atoms[a].index();
}
}
- }
-}
-
-void CS2Backbone::init_backbone(const PDB &pdb) {
- // number of chains
- vector<string> chains;
- pdb.getChainNames( chains );
- seg_last.resize(chains.size());
- unsigned old_size=0;
-
- for(unsigned i=0; i<chains.size(); i++) {
- unsigned start, end;
- string errmsg;
- pdb.getResidueRange( chains[i], start, end, errmsg );
- unsigned res_offset = start;
- unsigned resrange = end-start+1;
-
- if(i==0) seg_last[i] = resrange;
- else seg_last[i] = seg_last[i-1]+resrange;
-
- vector<int> N_;
- vector<int> H_;
- vector<int> CA_;
- vector<int> CB_;
- vector<int> HA_;
- vector<int> C_;
- vector<int> O_;
- vector<int> CX_;
- N_.resize (resrange,-1);
- H_.resize (resrange,-1);
- CA_.resize(resrange,-1);
- CB_.resize(resrange,-1);
- HA_.resize(resrange,-1);
- C_.resize (resrange,-1);
- O_.resize (resrange,-1);
- CX_.resize(resrange,-1);
-
- vector<AtomNumber> allatoms = pdb.getAtomsInChain(chains[i]);
- // cycle over all the atoms in the chain
- for(unsigned a=0; a<allatoms.size(); a++) {
- unsigned atm_index=a+old_size;
- unsigned f = pdb.getResidueNumber(allatoms[a]);
- unsigned f_idx = f-res_offset;
- string AN = pdb.getAtomName(allatoms[a]);
- string RES = pdb.getResidueName(allatoms[a]);
- if(AN=="N") N_ [f_idx] = atm_index;
- else if(AN=="H" ||AN=="HN" ) H_ [f_idx] = atm_index;
- else if(AN=="HA"||AN=="HA1") HA_[f_idx] = atm_index;
- else if(AN=="CA" ) CA_[f_idx] = atm_index;
- else if(AN=="CB" ) CB_[f_idx] = atm_index;
- else if(AN=="C" ) C_ [f_idx] = atm_index;
- else if(AN=="O" ) O_ [f_idx] = atm_index;
- else if(AN=="CD"&&RES=="PRO") H_[f_idx] = atm_index;
- if(is_chi1_cx(RES,AN)) CX_[f_idx] = atm_index;
+ vector<AtomNumber> next_res_atoms = pdb.getAtomsInResidue(resnum+1, chains[ichain]);
+ string NRES = pdb.getResidueName(resnum+1, chains[ichain]);
+ // find the position of the previous residues backbone atoms
+ for(unsigned a=0; a<next_res_atoms.size(); a++) {
+ string AN = pdb.getAtomName(next_res_atoms[a]);
+ if(AN=="N") { tmp_cs.bb[Nn] = next_res_atoms[a].index(); }
+ else if(AN=="H" ||AN=="HN"||(AN=="CD"&&NRES=="PRO")) { tmp_cs.bb[Hn] = next_res_atoms[a].index(); }
+ else if(AN=="CA") { tmp_cs.bb[CAn] = next_res_atoms[a].index(); }
+ else if(AN=="HA"||AN=="HA1"||AN=="HA3") { tmp_cs.bb[HAn] = next_res_atoms[a].index(); }
+ else if(AN=="C" ) { tmp_cs.bb[Cn] = next_res_atoms[a].index(); }
}
- old_size+=allatoms.size();
-
- // vector of residues for a given chain
- vector<Fragment> atm_;
- // cycle over all residues in the chain
- for(unsigned a=start; a<=end; a++) {
- unsigned f_idx = a - res_offset;
- Fragment at;
- at.pos[0] = HA_[f_idx];
- at.pos[1] = H_[f_idx];
- at.pos[2] = N_[f_idx];
- at.pos[3] = CA_[f_idx];
- at.pos[4] = CB_[f_idx];
- at.pos[5] = C_[f_idx];
- at.res_type_prev = at.res_type_curr = at.res_type_next = 0;
- at.res_name = pdb.getResidueName(a, chains[i]);
- at.res_kind = db.kind(at.res_name);
- at.fd = a;
- //REGISTER PREV CURR NEXT
- {
- if(a>start) {
- at.prev.push_back( N_[f_idx-1]);
- at.prev.push_back(CA_[f_idx-1]);
- at.prev.push_back(HA_[f_idx-1]);
- at.prev.push_back( C_[f_idx-1]);
- at.prev.push_back( O_[f_idx-1]);
- at.res_type_prev = frag2enum(pdb.getResidueName(a-1, chains[i]));
- }
-
- at.curr.push_back( N_[f_idx]);
- at.curr.push_back( H_[f_idx]);
- at.curr.push_back(CA_[f_idx]);
- at.curr.push_back(HA_[f_idx]);
- at.curr.push_back( C_[f_idx]);
- at.curr.push_back( O_[f_idx]);
- at.res_type_curr = frag2enum(pdb.getResidueName(a, chains[i]));
-
- if(a<end) {
- at.next.push_back (N_[f_idx+1]);
- at.next.push_back (H_[f_idx+1]);
- at.next.push_back(CA_[f_idx+1]);
- at.next.push_back(HA_[f_idx+1]);
- at.next.push_back( C_[f_idx+1]);
- at.res_type_next = frag2enum(pdb.getResidueName(a+1, chains[i]));
- }
- //PHI | PSI | CH1
- if(a>start) {
- at.phi.push_back( C_[f_idx-1]);
- at.phi.push_back( N_[f_idx]);
- at.phi.push_back(CA_[f_idx]);
- at.phi.push_back( C_[f_idx]);
- }
-
- if(a<end) {
- at.psi.push_back( N_[f_idx]);
- at.psi.push_back(CA_[f_idx]);
- at.psi.push_back( C_[f_idx]);
- at.psi.push_back( N_[f_idx+1]);
- }
+ // set sidechain atoms
+ vector<string> sc_atm = side_chain_atoms(RES);
- if(CX_[f_idx]!=-1&&CB_[f_idx]!=-1) {
- at.chi1.push_back( N_[f_idx]);
- at.chi1.push_back(CA_[f_idx]);
- at.chi1.push_back(CB_[f_idx]);
- at.chi1.push_back(CX_[f_idx]);
+ for(unsigned sc=0; sc<sc_atm.size(); sc++) {
+ for(unsigned aa=0; aa<res_atoms.size(); aa++) {
+ if(pdb.getAtomName(res_atoms[aa])==sc_atm[sc]) {
+ tmp_cs.side_chain.push_back(res_atoms[aa].index());
}
}
- atm_.push_back(at);
}
- atom.push_back(atm_);
- }
-}
-void CS2Backbone::init_sidechain(const PDB &pdb) {
- vector<string> chains;
- pdb.getChainNames( chains );
- unsigned old_size=0;
- // cycle over chains
- for(unsigned s=0; s<atom.size(); s++) {
- AtomNumber astart, aend;
- string errmsg;
- pdb.getAtomRange( chains[s], astart, aend, errmsg );
- unsigned atom_offset = astart.index();
- // cycle over residues
- for(unsigned a=0; a<atom[s].size(); a++) {
- if(atom[s][a].res_name=="UNK") continue;
- vector<AtomNumber> atm = pdb.getAtomsInResidue(atom[s][a].fd, chains[s]);
- vector<string> sc_atm = side_chain_atoms(atom[s][a].res_name);
-
- for(unsigned sc=0; sc<sc_atm.size(); sc++) {
- for(unsigned aa=0; aa<atm.size(); aa++) {
- if(pdb.getAtomName(atm[aa])==sc_atm[sc]) {
- atom[s][a].side_chain.push_back(atm[aa].index()-atom_offset+old_size);
- }
- }
- }
+ // find atoms for extra distances
+ const string atomsP1[] = {"H", "H", "H", "C", "C", "C", "O", "O", "O", "N", "N", "N", "O", "O", "O", "N", "N", "N", "CG", "CG", "CG", "CG", "CG", "CG", "CG", "CA"};
+ const int resOffsetP1[] = { 0, 0, 0, -1, -1, -1, 0, 0, 0, 1, 1, 1, -1, -1, -1, 0, 0, 0, 0, 0, 0, 0, 0, -1, 1, -1};
- }
- old_size += aend.index()+1;
- }
-}
-
-void CS2Backbone::init_xdist(const PDB &pdb) {
- const string atomsP1[] = {"H", "H", "H", "C", "C", "C",
- "O", "O", "O", "N", "N", "N",
- "O", "O", "O", "N", "N", "N",
- "CG", "CG", "CG", "CG", "CG",
- "CG", "CG", "CA"
- };
+ const string atomsP2[] = {"HA", "C", "CB", "HA", "C", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "CB", "HA", "N", "C", "C", "N", "CA", "CA", "CA"};
+ const int resOffsetP2[] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, -1, -1, -1, -1, 0, 0, 0, -1, 1, 0, 0, 1};
- const int resOffsetP1 [] = {0, 0, 0, -1, -1, -1,
- 0, 0, 0, 1, 1, 1,
- -1, -1, -1, 0, 0, 0,
- 0, 0, 0, 0, 0, -1, 1, -1
- };
+ for(unsigned q=0; q<db.get_numXtraDists()-1; q++) {
+ vector<AtomNumber> at1;
+ if(resOffsetP1[q]== 0) at1 = res_atoms;
+ if(resOffsetP1[q]==-1) at1 = prev_res_atoms;
+ if(resOffsetP1[q]==+1) at1 = next_res_atoms;
- const string atomsP2[] = {"HA", "C", "CB", "HA", "C", "CB",
- "HA", "N", "CB", "HA", "N", "CB",
- "HA", "N", "CB", "HA", "N", "CB",
- "HA", "N", "C", "C", "N", "CA", "CA", "CA"
- };
+ vector<AtomNumber> at2;
+ if(resOffsetP2[q]== 0) at2 = res_atoms;
+ if(resOffsetP2[q]==-1) at2 = prev_res_atoms;
+ if(resOffsetP2[q]==+1) at2 = next_res_atoms;
- const int resOffsetP2 [] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, -1, -1, -1, -1, 0, 0, 0, -1, 1, 0, 0, 1};
+ int tmp1 = -1;
+ for(unsigned a=0; a<at1.size(); a++) {
+ string name = pdb.getAtomName(at1[a]);
+ xdist_name_map(name);
- vector<string> chains;
- pdb.getChainNames( chains );
- unsigned old_size=0;
- for(unsigned s=0; s<atom.size(); s++) {
- AtomNumber astart, aend;
- string errmsg;
- pdb.getAtomRange( chains[s], astart, aend, errmsg );
- unsigned atom_offset = astart.index();
-
- for(unsigned a=1; a<atom[s].size()-1; a++) {
- vector<AtomNumber> atm_curr = pdb.getAtomsInResidue(atom[s][a].fd,chains[s]);
- vector<AtomNumber> atm_prev = pdb.getAtomsInResidue(atom[s][a].fd-1,chains[s]);
- vector<AtomNumber> atm_next = pdb.getAtomsInResidue(atom[s][a].fd+1,chains[s]);
-
- for(unsigned q=0; q<db.get_numXtraDists()-1; q++) {
- vector<AtomNumber>::iterator at1, at1_end;
- vector<AtomNumber>::iterator at2, at2_end;
-
- bool init_p1=false;
- AtomNumber p1;
- bool init_p2=false;
- AtomNumber p2;
-
- if(resOffsetP1[q]== 0) { at1 = atm_curr.begin(); at1_end = atm_curr.end();}
- if(resOffsetP1[q]==-1) { at1 = atm_prev.begin(); at1_end = atm_prev.end();}
- if(resOffsetP1[q]==+1) { at1 = atm_next.begin(); at1_end = atm_next.end();}
- while(at1!=at1_end) {
- AtomNumber aa = *at1;
- ++at1;
- string name = pdb.getAtomName(aa);
-
- xdist_name_map(name);
-
- if(name==atomsP1[q]) {
- p1 = aa;
- init_p1=true;
- break;
- }
+ if(name==atomsP1[q]) {
+ tmp1 = at1[a].index();
+ break;
}
+ }
- if(resOffsetP2[q]== 0) { at2 = atm_curr.begin(); at2_end = atm_curr.end();}
- if(resOffsetP2[q]==-1) { at2 = atm_prev.begin(); at2_end = atm_prev.end();}
- if(resOffsetP2[q]==+1) { at2 = atm_next.begin(); at2_end = atm_next.end();}
- while(at2!=at2_end) {
- AtomNumber aa = *at2;
- ++at2;
- string name = pdb.getAtomName(aa);
-
- xdist_name_map(name);
+ int tmp2 = -1;
+ for(unsigned a=0; a<at2.size(); a++) {
+ string name = pdb.getAtomName(at2[a]);
+ xdist_name_map(name);
- if(name==atomsP2[q]) {
- p2 = aa;
- init_p2=true;
- break;
- }
+ if(name==atomsP2[q]) {
+ tmp2 = at2[a].index();
+ break;
}
- int add1 = -1;
- int add2 = -1;
- if(init_p1) add1=p1.index()-atom_offset+old_size;
- if(init_p2) add2=p2.index()-atom_offset+old_size;
- atom[s][a].xd1.push_back(add1);
- atom[s][a].xd2.push_back(add2);
}
+
+ tmp_cs.xd1.push_back(tmp1);
+ tmp_cs.xd2.push_back(tmp2);
}
- old_size += aend.index()+1;
+
+ // ready to add a new chemical shifts
+ tmp_cs.csatoms = 1 + 16 + tmp_cs.side_chain.size() + 2*tmp_cs.xd1.size();
+ if(tmp_cs.res_name!="ALA"&&tmp_cs.res_name!="GLY") tmp_cs.csatoms += 2;
+ chemicalshifts.push_back(tmp_cs);
}
+
+ in.close();
}
+// this assigns an atom-type to each atom of the pdb
void CS2Backbone::init_types(const PDB &pdb) {
vector<AtomNumber> aa = pdb.getAtomNumbers();
for(unsigned i=0; i<aa.size(); i++) {
@@ -1587,47 +828,48 @@ void CS2Backbone::init_types(const PDB &pdb) {
else if (atom_type == 'H') t = D_H;
else if (atom_type == 'N') t = D_N;
else if (atom_type == 'S') t = D_S;
- else plumed_merror("CS2Backbone:init_type: unknown atom type!\n");
+ else plumed_merror("Unknown atom type: " + atom_name);
} else {
if (atom_type == 'C') t = D_C2;
else if (atom_type == 'O') t = D_O2;
else if (atom_type == 'N') t = D_N2;
- else plumed_merror("CS2Backbone:init_type: unknown atom type!\n");
+ else plumed_merror("Unknown atom type: " + atom_name);
}
type.push_back(t);
}
}
-void CS2Backbone::init_rings(const PDB &pdb) {
-
+void CS2Backbone::init_rings(const PDB &pdb)
+{
const string pheTyr_n[] = {"CG","CD1","CE1","CZ","CE2","CD2"};
const string trp1_n[] = {"CD2","CE2","CZ2","CH2","CZ3","CE3"};
const string trp2_n[] = {"CG","CD1","NE1","CE2","CD2"};
const string his_n[] = {"CG","ND1","CD2","CE1","NE2"};
+ // number of chains
vector<string> chains;
pdb.getChainNames( chains );
- vector<AtomNumber> allatoms = pdb.getAtomNumbers();
- unsigned old_size=0;
+ unsigned total_rings_atoms = 0;
- for(unsigned s=0; s<atom.size(); s++) {
- AtomNumber astart, aend;
+ // cycle over chains
+ for(unsigned i=0; i<chains.size(); i++) {
+ unsigned start, end;
string errmsg;
- pdb.getAtomRange( chains[s], astart, aend, errmsg );
- unsigned atom_offset = astart.index();
- for(unsigned r=0; r<atom[s].size(); r++) {
- string frg = pdb.getResidueName(atom[s][r].fd);
+ pdb.getResidueRange( chains[i], start, end, errmsg );
+ // cycle over residues
+ for(unsigned res=start; res<end; res++) {
+ string frg = pdb.getResidueName(res, chains[i]);
if(!((frg=="PHE")||(frg=="TYR")||(frg=="TRP")||
(frg=="HIS")||(frg=="HIP")||(frg=="HID")||
(frg=="HIE")||(frg=="HSD")||(frg=="HSE")||
(frg=="HSP"))) continue;
- vector<AtomNumber> frg_atoms = pdb.getAtomsInResidue(atom[s][r].fd,chains[s]);
+ vector<AtomNumber> frg_atoms = pdb.getAtomsInResidue(res,chains[i]);
if(frg=="PHE"||frg=="TYR") {
RingInfo ri;
for(unsigned a=0; a<frg_atoms.size(); a++) {
- unsigned atm = frg_atoms[a].index()-atom_offset+old_size;
+ unsigned atm = frg_atoms[a].index();
for(unsigned aa=0; aa<6; aa++) {
if(pdb.getAtomName(frg_atoms[a])==pheTyr_n[aa]) {
ri.atom[aa] = atm;
@@ -1636,6 +878,7 @@ void CS2Backbone::init_rings(const PDB &pdb) {
}
}
ri.numAtoms = 6;
+ total_rings_atoms += 6;
if(frg=="PHE") ri.rtype = RingInfo::R_PHE;
if(frg=="TYR") ri.rtype = RingInfo::R_TYR;
ringInfo.push_back(ri);
@@ -1644,7 +887,7 @@ void CS2Backbone::init_rings(const PDB &pdb) {
//First ring
RingInfo ri;
for(unsigned a=0; a<frg_atoms.size(); a++) {
- unsigned atm = frg_atoms[a].index()-atom_offset+old_size;
+ unsigned atm = frg_atoms[a].index();
for(unsigned aa=0; aa<6; aa++) {
if(pdb.getAtomName(frg_atoms[a])==trp1_n[aa]) {
ri.atom[aa] = atm;
@@ -1653,12 +896,13 @@ void CS2Backbone::init_rings(const PDB &pdb) {
}
}
ri.numAtoms = 6;
+ total_rings_atoms += 6;
ri.rtype = RingInfo::R_TRP1;
ringInfo.push_back(ri);
//Second Ring
RingInfo ri2;
for(unsigned a=0; a<frg_atoms.size(); a++) {
- unsigned atm = frg_atoms[a].index()-atom_offset+old_size;
+ unsigned atm = frg_atoms[a].index();
for(unsigned aa=0; aa<5; aa++) {
if(pdb.getAtomName(frg_atoms[a])==trp2_n[aa]) {
ri2.atom[aa] = atm;
@@ -1667,6 +911,7 @@ void CS2Backbone::init_rings(const PDB &pdb) {
}
}
ri2.numAtoms = 5;
+ total_rings_atoms += 3;
ri2.rtype = RingInfo::R_TRP2;
ringInfo.push_back(ri2);
@@ -1675,7 +920,7 @@ void CS2Backbone::init_rings(const PDB &pdb) {
(frg=="HSP")) {//HIS case
RingInfo ri;
for(unsigned a=0; a<frg_atoms.size(); a++) {
- unsigned atm = frg_atoms[a].index()-atom_offset+old_size;
+ unsigned atm = frg_atoms[a].index();
for(unsigned aa=0; aa<5; aa++) {
if(pdb.getAtomName(frg_atoms[a])==his_n[aa]) {
ri.atom[aa] = atm;
@@ -1684,18 +929,479 @@ void CS2Backbone::init_rings(const PDB &pdb) {
}
}
ri.numAtoms = 5;
+ total_rings_atoms += 3;
ri.rtype = RingInfo::R_HIS;
ringInfo.push_back(ri);
} else {
- plumed_merror("Unkwown Ring Fragment");
+ plumed_merror("Unknown Ring Fragment: " + frg);
}
}
- old_size += aend.index()+1;
}
+
+ for(unsigned cs=0; cs<chemicalshifts.size(); cs++) chemicalshifts[cs].csatoms += total_rings_atoms;
}
-CS2Backbone::aa_t CS2Backbone::frag2enum(const string &aa) {
+void CS2Backbone::calculate()
+{
+ if(pbc) makeWhole();
+ if(getExchangeStep()) box_count=0;
+ if(box_count==0) update_neighb();
+ compute_ring_parameters();
+
+ vector<double> camshift_sigma2(6);
+ camshift_sigma2[0] = 0.08; // HA
+ camshift_sigma2[1] = 0.30; // HN
+ camshift_sigma2[2] = 9.00; // NH
+ camshift_sigma2[3] = 1.30; // CA
+ camshift_sigma2[4] = 1.56; // CB
+ camshift_sigma2[5] = 1.70; // CO
+
+ vector<Vector> cs_derivs;
+ vector<Vector> aa_derivs;
+ vector<unsigned> cs_atoms;
+ vector<double> all_shifts;
+
+ cs_derivs.resize(chemicalshifts.size()*max_cs_atoms,Vector(0,0,0));
+ cs_atoms.resize(chemicalshifts.size()*max_cs_atoms,0);
+ all_shifts.resize(chemicalshifts.size(),0);
+ if(camshift||getDoScore()) aa_derivs.resize(getNumberOfAtoms(),Vector(0,0,0));
+
+ unsigned stride = comm.Get_size();
+ unsigned rank = comm.Get_rank();
+ if(serial) {
+ stride = 1;
+ rank = 0;
+ }
+
+ double score = 0.;
+
+ // a single loop over all chemical shifts
+ for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
+ const unsigned kdx=cs*max_cs_atoms;
+ const ChemicalShift *myfrag = &chemicalshifts[cs];
+ const unsigned aa_kind = myfrag->res_kind;
+ const unsigned at_kind = myfrag->atm_kind;
+ // Common constant and AATYPE
+ const double * CONSTAACURR = db.CONSTAACURR(aa_kind,at_kind);
+ const double * CONSTAANEXT = db.CONSTAANEXT(aa_kind,at_kind);
+ const double * CONSTAAPREV = db.CONSTAAPREV(aa_kind,at_kind);
+
+ double shift = CONSTAAPREV[myfrag->res_type_prev] +
+ CONSTAACURR[myfrag->res_type_curr] +
+ CONSTAANEXT[myfrag->res_type_next];
+
+ const unsigned ipos = myfrag->ipos;
+ cs_atoms[kdx+0] = ipos;
+ unsigned atom_counter = 1;
+
+ //BACKBONE (PREV CURR NEXT)
+ const double * CONST_BB2 = db.CONST_BB2(aa_kind,at_kind);
+ const unsigned bbsize = 16;
+ for(unsigned q=0; q<bbsize; q++) {
+ const double cb2q = CONST_BB2[q];
+ if(cb2q==0.) continue;
+ const unsigned jpos = myfrag->bb[q];
+ if(ipos==jpos) continue;
+ const Vector distance = delta(getPosition(jpos),getPosition(ipos));
+ const double d = distance.modulo();
+ const double fact = cb2q/d;
+
+ shift += cb2q*d;
+ const Vector der = fact*distance;
+
+ cs_derivs[kdx+0] += der;
+ cs_derivs[kdx+q+atom_counter] = -der;
+ cs_atoms[kdx+q+atom_counter] = jpos;
+ }
+
+ atom_counter += bbsize;
+
+ //DIHEDRAL ANGLES
+ const double *CO_DA = db.CO_DA(aa_kind,at_kind);
+ //Phi
+ {
+ const Vector d0 = delta(getPosition(myfrag->bb[Nc]), getPosition(myfrag->bb[Cp]));
+ const Vector d1 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
+ const Vector d2 = delta(getPosition(myfrag->bb[Cc]), getPosition(myfrag->bb[CAc]));
+ Torsion t;
+ Vector dd0, dd1, dd2;
+ const double t_phi = t.compute(d0,d1,d2,dd0,dd1,dd2);
+ const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,0);
+ const double val1 = 3.*t_phi+PARS_DA[3];
+ const double val2 = t_phi+PARS_DA[4];
+ shift += CO_DA[0]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
+ const double fact = -CO_DA[0]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
+
+ cs_derivs[kdx+Cp+1] += fact*dd0;
+ cs_derivs[kdx+Nc+1] += fact*(dd1-dd0);
+ cs_derivs[kdx+CAc+1]+= fact*(dd2-dd1);
+ cs_derivs[kdx+Cc+1] += -fact*dd2;
+ cs_atoms[kdx+Cp+1] = myfrag->bb[Cp];
+ cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
+ cs_atoms[kdx+CAc+1]= myfrag->bb[CAc];
+ cs_atoms[kdx+Cc+1] = myfrag->bb[Cc];
+ }
+
+ //Psi
+ {
+ const Vector d0 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
+ const Vector d1 = delta(getPosition(myfrag->bb[Cc]), getPosition(myfrag->bb[CAc]));
+ const Vector d2 = delta(getPosition(myfrag->bb[Nn]), getPosition(myfrag->bb[Cc]));
+ Torsion t;
+ Vector dd0, dd1, dd2;
+ const double t_psi = t.compute(d0,d1,d2,dd0,dd1,dd2);
+ const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,1);
+ const double val1 = 3.*t_psi+PARS_DA[3];
+ const double val2 = t_psi+PARS_DA[4];
+ shift += CO_DA[1]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
+ const double fact = -CO_DA[1]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
+
+ cs_derivs[kdx+Nc+1] += fact*dd0;
+ cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);
+ cs_derivs[kdx+Cc+1] += fact*(dd2-dd1);
+ cs_derivs[kdx+Nn+1] += -fact*dd2;
+ cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
+ cs_atoms[kdx+CAc+1]= myfrag->bb[CAc];
+ cs_atoms[kdx+Cc+1] = myfrag->bb[Cc];
+ cs_atoms[kdx+Nn+1] = myfrag->bb[Nn];
+ }
+
+ //Chi
+ if(myfrag->has_chi1) {
+ const Vector d0 = delta(getPosition(myfrag->bb[CAc]), getPosition(myfrag->bb[Nc]));
+ const Vector d1 = delta(getPosition(myfrag->bb[CBc]), getPosition(myfrag->bb[CAc]));
+ const Vector d2 = delta(getPosition(myfrag->bb[CGc]), getPosition(myfrag->bb[CBc]));
+ Torsion t;
+ Vector dd0, dd1, dd2;
+ const double t_chi1 = t.compute(d0,d1,d2,dd0,dd1,dd2);
+ const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,2);
+ const double val1 = 3.*t_chi1+PARS_DA[3];
+ const double val2 = t_chi1+PARS_DA[4];
+ shift += CO_DA[2]*(PARS_DA[0]*cos(val1)+PARS_DA[1]*cos(val2)+PARS_DA[2]);
+ const double fact = -CO_DA[2]*(+3.*PARS_DA[0]*sin(val1)+PARS_DA[1]*sin(val2));
+
+ cs_derivs[kdx+Nc+1] += fact*dd0;
+ cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);
+ cs_derivs[kdx+CBc+1] += fact*(dd2-dd1);
+ cs_derivs[kdx+CGc+1] += -fact*dd2;
+ cs_atoms[kdx+Nc+1] = myfrag->bb[Nc];
+ cs_atoms[kdx+CAc+1] = myfrag->bb[CAc];
+ cs_atoms[kdx+CBc+1] = myfrag->bb[CBc];
+ cs_atoms[kdx+CGc+1] = myfrag->bb[CGc];
+
+ atom_counter += 2;
+ }
+ //END OF DIHE
+
+ //SIDE CHAIN
+ const double * CONST_SC2 = db.CONST_SC2(aa_kind,at_kind,myfrag->res_type_curr);
+ const unsigned sidsize = myfrag->side_chain.size();
+ for(unsigned q=0; q<sidsize; q++) {
+ const double cs2q = CONST_SC2[q];
+ if(cs2q==0.) continue;
+ const unsigned jpos = myfrag->side_chain[q];
+ if(ipos==jpos) continue;
+ const Vector distance = delta(getPosition(jpos),getPosition(ipos));
+ const double d = distance.modulo();
+ const double fact = cs2q/d;
+
+ shift += cs2q*d;
+ const Vector der = fact*distance;
+ cs_derivs[kdx+0] += der;
+ cs_derivs[kdx+q+atom_counter] = -der;
+ cs_atoms[kdx+q+atom_counter] = jpos;
+ }
+
+ atom_counter += sidsize;
+
+ //EXTRA DIST
+ const double * CONST_XD = db.CONST_XD(aa_kind,at_kind);
+ const unsigned xdsize=myfrag->xd1.size();
+ for(unsigned q=0; q<xdsize; q++) {
+ const double cxdq = CONST_XD[q];
+ if(cxdq==0.) continue;
+ if(myfrag->xd1[q]==-1||myfrag->xd2[q]==-1) continue;
+ const Vector distance = delta(getPosition(myfrag->xd1[q]),getPosition(myfrag->xd2[q]));
+ const double d = distance.modulo();
+ const double fact = cxdq/d;
+
+ shift += cxdq*d;
+ const Vector der = fact*distance;
+ cs_derivs[kdx+2*q+atom_counter ] = der;
+ cs_derivs[kdx+2*q+atom_counter+1] = -der;
+ cs_atoms[kdx+2*q+atom_counter] = myfrag->xd2[q];
+ cs_atoms[kdx+2*q+atom_counter+1] = myfrag->xd1[q];
+ }
+
+ atom_counter += 2*xdsize;
+
+ //RINGS
+ const double *rc = db.CO_RING(aa_kind,at_kind);
+ const unsigned rsize = ringInfo.size();
+ // cycle over the list of rings
+ for(unsigned q=0; q<rsize; q++) {
+ // compute angle from ring middle point to current atom position
+ // get distance vector from query atom to ring center and normal vector to ring plane
+ const Vector n = ringInfo[q].normVect;
+ const double nL = ringInfo[q].lengthNV;
+ const double inL2 = ringInfo[q].lengthN2;
+
+ const Vector d = delta(ringInfo[q].position, getPosition(ipos));
+ const double dL2 = d.modulo2();
+ double dL = sqrt(dL2);
+ const double idL3 = 1./(dL2*dL);
+
+ const double dn = dotProduct(d,n);
+ const double dn2 = dn*dn;
+ const double dLnL = dL*nL;
+ const double dL_nL = dL/nL;
+
+ const double ang2 = dn2*inL2/dL2;
+ const double u = 1.-3.*ang2;
+ const double cc = rc[ringInfo[q].rtype];
+
+ shift += cc*u*idL3;
+
+ const double fUU = -6*dn*inL2;
+ const double fUQ = fUU/dL;
+ const Vector gradUQ = fUQ*(dL2*n - dn*d);
+ const Vector gradVQ = (3*dL*u)*d;
+
+ const double fact = cc*idL3*idL3;
+ cs_derivs[kdx+0] += fact*(gradUQ - gradVQ);
+
+ const double fU = fUU/nL;
+ double OneOverN = 1./6.;
+ if(ringInfo[q].numAtoms==5) OneOverN=1./3.;
+ const Vector factor2 = OneOverN*n;
+ const Vector factor4 = (OneOverN/dL_nL)*d;
+
+ const Vector gradV = -OneOverN*gradVQ;
+
+ if(ringInfo[q].numAtoms==6) {
+ // update forces on ring atoms
+ for(unsigned at=0; at<6; at++) {
+ const Vector ab = crossProduct(d,ringInfo[q].g[at]);
+ const Vector c = crossProduct(n,ringInfo[q].g[at]);
+ const Vector factor3 = 0.5*dL_nL*c;
+ const Vector factor1 = 0.5*ab;
+ const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
+ cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);
+ cs_atoms[kdx+at+atom_counter] = ringInfo[q].atom[at];
+ }
+ atom_counter += 6;
+ } else {
+ for(unsigned at=0; at<3; at++) {
+ const Vector ab = crossProduct(d,ringInfo[q].g[at]);
+ const Vector c = crossProduct(n,ringInfo[q].g[at]);
+ const Vector factor3 = dL_nL*c;
+ const Vector factor1 = ab;
+ const Vector gradU = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );
+ cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);
+ }
+ cs_atoms[kdx+atom_counter] = ringInfo[q].atom[0];
+ cs_atoms[kdx+atom_counter+1] = ringInfo[q].atom[2];
+ cs_atoms[kdx+atom_counter+2] = ringInfo[q].atom[3];
+ atom_counter += 3;
+ }
+ }
+ //END OF RINGS
+
+ //NON BOND
+ const double * CONST_CO_SPHERE3 = db.CO_SPHERE(aa_kind,at_kind,0);
+ const double * CONST_CO_SPHERE = db.CO_SPHERE(aa_kind,at_kind,1);
+ const unsigned boxsize = myfrag->box_nb.size();
+ for(unsigned q=0; q<boxsize; q++) {
+ const unsigned jpos = myfrag->box_nb[q];
+ const Vector distance = delta(getPosition(jpos),getPosition(ipos));
+ const double d2 = distance.modulo2();
+
+ if(d2<cutOffDist2) {
+ double factor1 = sqrt(d2);
+ double dfactor1 = 1./factor1;
+ double factor3 = dfactor1*dfactor1*dfactor1;
+ double dfactor3 = -3.*factor3*dfactor1*dfactor1;
+
+ if(d2>cutOnDist2) {
+ const double af = cutOffDist2 - d2;
+ const double bf = cutOffDist2 - 3.*cutOnDist2 + 2.*d2;
+ const double cf = invswitch*af;
+ const double df = cf*af*bf;
+ factor1 *= df;
+ factor3 *= df;
+
+ const double d4 = d2*d2;
+ const double af1 = 15.*cutOnDist2*d2;
+ const double bf1 = -14.*d4;
+ const double cf1 = -3.*cutOffDist2*cutOnDist2 + cutOffDist2*d2;
+ const double df1 = af1+bf1+cf1;
+ dfactor1 *= cf*(cutOffDist4+df1);
+
+ const double af3 = +2.*cutOffDist2*cutOnDist2;
+ const double bf3 = d2*(cutOffDist2+cutOnDist2);
+ const double cf3 = -2.*d4;
+ const double df3 = (af3+bf3+cf3)*d2;
+ dfactor3 *= invswitch*(cutMixed+df3);
+ }
+
+ const unsigned t = type[jpos];
+ shift += factor1*CONST_CO_SPHERE[t] + factor3*CONST_CO_SPHERE3[t] ;
+ const double fact = dfactor1*CONST_CO_SPHERE[t]+dfactor3*CONST_CO_SPHERE3[t];
+ const Vector der = fact*distance;
+
+ cs_derivs[kdx+0] += der;
+ cs_derivs[kdx+q+atom_counter] = -der;
+ cs_atoms[kdx+q+atom_counter] = jpos;
+ }
+ }
+ //END NON BOND
+
+ atom_counter += boxsize;
+ all_shifts[cs] = shift;
+
+ if(camshift) {
+ score += (all_shifts[cs] - chemicalshifts[cs].exp_cs)*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];
+ double fact = 2.0*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];
+ for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;
+ }
+ }
+
+ if(!camshift) {
+ if(!serial) {
+ if(!getDoScore()) {
+ comm.Sum(&cs_derivs[0][0], 3*cs_derivs.size());
+ comm.Sum(&cs_atoms[0], cs_atoms.size());
+ }
+ comm.Sum(&all_shifts[0], chemicalshifts.size());
+ }
+ for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
+ Value *comp = chemicalshifts[cs].comp;
+ comp->set(all_shifts[cs]);
+ if(getDoScore()) setCalcData(cs, all_shifts[cs]);
+ else {
+ const unsigned kdx=cs*max_cs_atoms;
+ Tensor virial;
+ for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
+ setAtomsDerivatives(comp,cs_atoms[kdx+i],cs_derivs[kdx+i]);
+ virial-=Tensor(getPosition(cs_atoms[kdx+i]),cs_derivs[kdx+i]);
+ }
+ setBoxDerivatives(comp,virial);
+ }
+ }
+ if(!getDoScore()) return;
+ }
+
+ /* Metainference */
+ if(getDoScore()) {
+ score = getScore();
+ for(unsigned cs=rank; cs<chemicalshifts.size(); cs+=stride) {
+ const unsigned kdx=cs*max_cs_atoms;
+ const double fact = getMetaDer(cs);
+ for(unsigned i=0; i<chemicalshifts[cs].totcsatoms; i++) {
+ aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;
+ }
+ }
+ }
+
+ if(!serial) {
+ comm.Sum(&aa_derivs[0][0], 3*aa_derivs.size());
+ if(camshift) comm.Sum(&score, 1);
+ }
+
+ /* calculate final derivatives */
+ Value* val;
+ if(getDoScore()) {
+ val=getPntrToComponent("score");
+ setScore(score);
+ } else {
+ val=getPntrToValue();
+ setValue(score);
+ }
+
+ Tensor virial;
+ /* at this point we cycle over all atoms */
+ for(unsigned i=0; i<getNumberOfAtoms(); i++) {
+ setAtomsDerivatives(val, i, aa_derivs[i]);
+ virial-=Tensor(getPosition(i), aa_derivs[i]);
+ }
+ setBoxDerivatives(val,virial);
+
+ ++box_count;
+ if(box_count == box_nupdate) box_count = 0;
+}
+
+void CS2Backbone::update_neighb() {
+ max_cs_atoms=0;
+ // cycle over chemical shifts
+ #pragma omp parallel for num_threads(OpenMP::getNumThreads())
+ for(unsigned cs=0; cs<chemicalshifts.size(); cs++) {
+ const unsigned boxsize = getNumberOfAtoms();
+ chemicalshifts[cs].box_nb.clear();
+ chemicalshifts[cs].box_nb.reserve(150);
+ const unsigned res_curr = res_num[chemicalshifts[cs].ipos];
+ for(unsigned bat=0; bat<boxsize; bat++) {
+ const unsigned res_dist = abs(static_cast<int>(res_curr-res_num[bat]));
+ if(res_dist<2) continue;
+ const Vector distance = delta(getPosition(bat),getPosition(chemicalshifts[cs].ipos));
+ const double d2=distance.modulo2();
+ if(d2<cutOffNB2) chemicalshifts[cs].box_nb.push_back(bat);
+ }
+ chemicalshifts[cs].totcsatoms = chemicalshifts[cs].csatoms + chemicalshifts[cs].box_nb.size();
+ if(chemicalshifts[cs].totcsatoms>max_cs_atoms) max_cs_atoms = chemicalshifts[cs].totcsatoms;
+ }
+}
+
+void CS2Backbone::compute_ring_parameters() {
+ for(unsigned i=0; i<ringInfo.size(); i++) {
+ const unsigned size = ringInfo[i].numAtoms;
+ if(size==6) {
+ ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[4]),getPosition(ringInfo[i].atom[2]));
+ ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[5]),getPosition(ringInfo[i].atom[3]));
+ ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[4]));
+ ringInfo[i].g[3] = delta(getPosition(ringInfo[i].atom[1]),getPosition(ringInfo[i].atom[5]));
+ ringInfo[i].g[4] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
+ ringInfo[i].g[5] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[1]));
+ vector<Vector> a(size);
+ a[0] = getPosition(ringInfo[i].atom[0]);
+ // ring center
+ Vector midP = a[0];
+ for(unsigned j=1; j<size; j++) {
+ a[j] = getPosition(ringInfo[i].atom[j]);
+ midP += a[j];
+ }
+ midP /= (double) size;
+ ringInfo[i].position = midP;
+ // compute normal vector to plane containing first three atoms in array
+ ringInfo[i].n1 = crossProduct(delta(a[0],a[4]), delta(a[0],a[2]));
+ // compute normal vector to plane containing last three atoms in array
+ // NB: third atom of five-membered ring used for both computations above
+ ringInfo[i].n2 = crossProduct(delta(a[3],a[1]), delta(a[3],a[5]));
+ // ring plane normal vector is average of n1 and n2
+ ringInfo[i].normVect = 0.5*(ringInfo[i].n1 + ringInfo[i].n2);
+ } else {
+ ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[2]));
+ ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[3]));
+ ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));
+ vector<Vector> a(size);
+ for(unsigned j=0; j<size; j++) {
+ a[j] = getPosition(ringInfo[i].atom[j]);
+ }
+ // ring center
+ Vector midP = (a[0]+a[2]+a[3])/3.;
+ ringInfo[i].position = midP;
+ // compute normal vector to plane containing first three atoms in array
+ ringInfo[i].n1 = crossProduct(delta(a[0],a[3]), delta(a[0],a[2]));
+ // ring plane normal vector is average of n1 and n2
+ ringInfo[i].normVect = ringInfo[i].n1;
+ }
+ // calculate squared length and length of normal vector
+ ringInfo[i].lengthN2 = 1./ringInfo[i].normVect.modulo2();
+ ringInfo[i].lengthNV = 1./sqrt(ringInfo[i].lengthN2);
+ }
+}
+
+CS2Backbone::aa_t CS2Backbone::frag2enum(const string &aa) {
aa_t type = ALA;
if (aa == "ALA") type = ALA;
else if (aa == "ARG") type = ARG;
@@ -1727,7 +1433,7 @@ CS2Backbone::aa_t CS2Backbone::frag2enum(const string &aa) {
else if (aa == "TYR") type = TYR;
else if (aa == "VAL") type = VAL;
else if (aa == "UNK") type = UNK;
- else plumed_merror("CS2Backbone: Error converting string " + aa + " into amino acid index: not a valid 3-letter code");
+ else plumed_merror("Error converting string " + aa + " into amino acid index: not a valid 3-letter code");
return type;
}
@@ -2040,7 +1746,7 @@ vector<string> CS2Backbone::side_chain_atoms(const string &s) {
sc.push_back( "2HG2" );
sc.push_back( "3HG2" );
return sc;
- } else plumed_merror("CS2Backbone: side_chain_atoms unknown");
+ } else plumed_merror("Sidechain atoms unknown: " + s);
}
bool CS2Backbone::isSP2(const string & resType, const string & atomName) {
@@ -2049,7 +1755,6 @@ bool CS2Backbone::isSP2(const string & resType, const string & atomName) {
if (atomName == "O") return true;
if(resType == "TRP") {
-
if (atomName == "CG") sp2 = true;
else if (atomName == "CD1") sp2 = true;
else if (atomName == "CD2") sp2 = true;
@@ -2058,59 +1763,42 @@ bool CS2Backbone::isSP2(const string & resType, const string & atomName) {
else if (atomName == "CZ2") sp2 = true;
else if (atomName == "CZ3") sp2 = true;
else if (atomName == "CH2") sp2 = true;
-
} else if (resType == "ASP") {
-
if (atomName == "CG") sp2 = true;
else if (atomName == "OD1") sp2 = true;
else if (atomName == "OD2") sp2 = true;
-
} else if (resType == "GLU") {
-
if (atomName == "CD") sp2 = true;
else if (atomName == "OE1") sp2 = true;
else if (atomName == "OE2") sp2 = true;
-
} else if (resType == "ARG") {
-
if (atomName == "CZ") sp2 = true;
-
} else if (resType == "HIS") {
-
if (atomName == "CG") sp2 = true;
else if (atomName == "ND1") sp2 = true;
else if (atomName == "CD2") sp2 = true;
else if (atomName == "CE1") sp2 = true;
else if (atomName == "NE2") sp2 = true;
-
} else if (resType == "PHE") {
-
if (atomName == "CG") sp2 = true;
else if (atomName == "CD1") sp2 = true;
else if (atomName == "CD2") sp2 = true;
else if (atomName == "CE1") sp2 = true;
else if (atomName == "CE2") sp2 = true;
else if (atomName == "CZ") sp2 = true;
-
} else if (resType == "TYR") {
-
if (atomName == "CG") sp2 = true;
else if (atomName == "CD1") sp2 = true;
else if (atomName == "CD2") sp2 = true;
else if (atomName == "CE1") sp2 = true;
else if (atomName == "CE2") sp2 = true;
else if (atomName == "CZ") sp2 = true;
-
} else if (resType == "ASN") {
-
if (atomName == "CG") sp2 = true;
else if (atomName == "OD1") sp2 = true;
-
} else if (resType == "GLN") {
-
if (atomName == "CD") sp2 = true;
else if (atomName == "OE1") sp2 = true;
-
}
return sp2;
@@ -2126,72 +1814,12 @@ bool CS2Backbone::is_chi1_cx(const string & frg, const string & atm) {
return false;
}
-unsigned CS2Backbone::frag_segment(const unsigned p) {
- unsigned s = 0;
- for(unsigned i=0; i<seg_last.size()-1; i++) {
- if(p>seg_last[i]) s = i+1;
- else break;
- }
- return s;
-}
-
-unsigned CS2Backbone::frag_relitive_index(const unsigned p, const unsigned s) {
- if(s==0) return p;
- return p-seg_last[s-1];
-}
-
-void CS2Backbone::debug_report() {
- printf("\t CS2Backbone Initialization report: \n");
- printf("\t -------------------------------\n");
- printf("\t Number of segments: %u\n", static_cast<unsigned>(atom.size()));
- printf("\t Segments size: ");
- for(unsigned i=0; i<atom.size(); i++) printf("%u ", static_cast<unsigned>(atom[i].size())); printf("\n");
- printf("\t%8s %8s %8s %8s %8s %8s %8s %8s %8s %8s %8s %8s \n",
- "Seg","N","AA","Prev","Curr","Next","SC","XD1","XD2","Phi","Psi","Chi1");
- for(unsigned i=0; i<atom.size(); i++) {
- for(unsigned j=0; j<atom[i].size(); j++) {
- printf("\t%8u %8u %8s %8u %8u %8u %8u %8u %8u %8u %8u %8u \n",
- i+1, j+1,
- atom[i][j].res_name.c_str(),
- (unsigned)atom[i][j].prev.size(),
- (unsigned)atom[i][j].curr.size(),
- (unsigned)atom[i][j].next.size(),
- (unsigned)atom[i][j].side_chain.size(),
- (unsigned)atom[i][j].xd1.size(),
- (unsigned)atom[i][j].xd2.size(),
- (unsigned)atom[i][j].phi.size(),
- (unsigned)atom[i][j].psi.size(),
- (unsigned)atom[i][j].chi1.size());
-
- for(unsigned k=0; k<atom[i][j].prev.size(); k++) printf("%8i ", atom[i][j].prev[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].curr.size(); k++) printf("%8i ", atom[i][j].curr[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].next.size(); k++) printf("%8i ", atom[i][j].next[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].side_chain.size(); k++) printf("%8i ", atom[i][j].side_chain[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].xd1.size(); k++) printf("%8i ", atom[i][j].xd1[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].xd2.size(); k++) printf("%8i ", atom[i][j].xd2[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].phi.size(); k++) printf("%8i ", atom[i][j].phi[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].psi.size(); k++) printf("%8i ", atom[i][j].psi[k]); printf("\n");
- for(unsigned k=0; k<atom[i][j].chi1.size(); k++) printf("%8i ", atom[i][j].chi1[k]); printf("\n");
-
- }
- }
-
- printf("\t Rings: \n");
- printf("\t ------ \n");
- printf("\t Number of rings: %u\n", static_cast<unsigned>(ringInfo.size()));
- printf("\t%8s %8s %8s %8s\n", "Num","Type","RType","N.atoms");
- for(unsigned i=0; i<ringInfo.size(); i++) {
- printf("\t%8u %8u %8u \n",i+1,ringInfo[i].rtype,ringInfo[i].numAtoms);
- for(unsigned j=0; j<ringInfo[i].numAtoms; j++) printf("%8u ", ringInfo[i].atom[j]); printf("\n");
- }
-}
-
void CS2Backbone::xdist_name_map(string & name) {
if((name == "OT1")||(name == "OC1")) name = "O";
else if ((name == "HN") || (name == "HT1") || (name == "H1")) name = "H";
else if ((name == "CG1")|| (name == "OG")||
(name == "SG") || (name == "OG1")) name = "CG";
- else if ((name == "HA1")) name = "HA";
+ else if ((name == "HA1")|| (name == "HA3")) name = "HA";
}
void CS2Backbone::update() {
diff --git a/src/isdb/EMMI.cpp b/src/isdb/EMMI.cpp
index 313287ab108ee22a80d1afbe1fe96dc78b72cb41..5c49e5e9a7925eae5fa3c8fa7f792e7aba88b91c 100644
--- a/src/isdb/EMMI.cpp
+++ b/src/isdb/EMMI.cpp
@@ -336,6 +336,7 @@ EMMI::EMMI(const ActionOptions&ao):
log<<" Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
log<<plumed.cite("Hanot, Bonomi, Greenberg, Sali, Nilges, Vendruscolo, Pellarin, bioRxiv doi: 10.1101/113951 (2017)");
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
}
diff --git a/src/isdb/FretEfficiency.cpp b/src/isdb/FretEfficiency.cpp
index 079ee9b7a64efd91be88bb31e8da3bd02d2a13a4..828e0ba2424db1fb0728cc9a6741536af6ea837f 100644
--- a/src/isdb/FretEfficiency.cpp
+++ b/src/isdb/FretEfficiency.cpp
@@ -21,6 +21,7 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "colvar/Colvar.h"
#include "colvar/ActionRegister.h"
+#include "core/PlumedMain.h"
#include "tools/Pbc.h"
#include <string>
@@ -119,6 +120,8 @@ FretEfficiency::FretEfficiency(const ActionOptions&ao):
if(pbc) log.printf(" using periodic boundary conditions\n");
else log.printf(" without periodic boundary conditions\n");
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
addValueWithDerivatives();
setNotPeriodic();
diff --git a/src/isdb/Jcoupling.cpp b/src/isdb/Jcoupling.cpp
index da0df77d282c4ffdcf06649f48428f08e4fc0877..c335a50eae0d527873cbb9f557c1c82f49cb132c 100644
--- a/src/isdb/Jcoupling.cpp
+++ b/src/isdb/Jcoupling.cpp
@@ -21,8 +21,6 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include "tools/Torsion.h"
@@ -169,7 +167,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
ncoupl_ = atoms.size()/6;
// Parse J-Coupling type, this will determine the Karplus parameters
- unsigned jtype_;
+ unsigned jtype_ = CUSTOM;
string string_type;
parse("TYPE", string_type);
if(string_type == "HAN") {
@@ -212,6 +210,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
parse("SHIFT", kshift_);
}
+ log << " Bibliography ";
// Set Karplus parameters
switch (jtype_) {
@@ -221,8 +220,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = -0.27;
kshift_ = pi / 3.0;
log.printf("J-coupling type is HAN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)") << "\n";
+ log << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)");
break;
case HAHN:
ka_ = 7.09;
@@ -230,8 +228,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = 1.55;
kshift_ = -pi / 3.0;
log.printf("J-coupling type is HAHN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)") << "\n";
+ log << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)");
break;
case CCG:
ka_ = 2.31;
@@ -239,8 +236,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = 0.55;
kshift_ = (2.0 * pi) / 3.0;
log.printf("J-coupling type is CCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)") << "\n";
+ log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
break;
case NCG:
ka_ = 1.29;
@@ -248,13 +244,14 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = 0.37;
kshift_ = 0.0;
log.printf("J-coupling type is NCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)") << "\n";
+ log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
break;
case CUSTOM:
log.printf("J-coupling type is custom, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
break;
}
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
+ log<<"\n";
for (unsigned i = 0; i < ncoupl_; ++i) {
log.printf(" The %uth J-Coupling is calculated from atoms : %d %d %d %d.",
diff --git a/src/isdb/Metainference.cpp b/src/isdb/Metainference.cpp
index f9ea30effadfb8118cb22615accbd093a166bc8f..2536c0f50f6295da04275a7d34ac65713301cb6c 100644
--- a/src/isdb/Metainference.cpp
+++ b/src/isdb/Metainference.cpp
@@ -752,6 +752,7 @@ Metainference::Metainference(const ActionOptions&ao):
log<<" Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
if(do_reweight_) log<<plumed.cite("Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)");
if(do_optsigmamean_>0) log<<plumed.cite("Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)");
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
}
@@ -1085,7 +1086,7 @@ void Metainference::doMonteCarlo(const vector<double> &mean_)
}
// calculate new energy
- double new_energy;
+ double new_energy = 0.;
switch(noise_type_) {
case GAUSS:
new_energy = getEnergyGJ(mean_,new_sigma,scale_,offset_);
diff --git a/src/isdb/MetainferenceBase.cpp b/src/isdb/MetainferenceBase.cpp
index 36f2493ffcc704f0c66dc1e84bc5c934c37b3a4f..381fa96b34f35c9004b0b3ea9230ae63c35a1af8 100644
--- a/src/isdb/MetainferenceBase.cpp
+++ b/src/isdb/MetainferenceBase.cpp
@@ -20,9 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "MetainferenceBase.h"
-#include "core/PlumedMain.h"
#include "tools/File.h"
-#include "tools/OpenMP.h"
#include <cmath>
#include <ctime>
#include <numeric>
@@ -552,6 +550,7 @@ void MetainferenceBase::Initialise(const unsigned input)
log<<" Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
if(do_reweight_) log<<plumed.cite("Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)");
if(do_optsigmamean_>0) log<<plumed.cite("Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)");
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
}
@@ -889,7 +888,7 @@ void MetainferenceBase::doMonteCarlo(const vector<double> &mean_)
}
// calculate new energy
- double new_energy;
+ double new_energy=0.;
switch(noise_type_) {
case GAUSS:
new_energy = getEnergyGJ(mean_,new_sigma,scale_,offset_);
diff --git a/src/isdb/MetainferenceBase.h b/src/isdb/MetainferenceBase.h
index f5b3f686ff70942e1810f2e02afcd4f3c4a065ca..7594d2b98dca99d21b3a608df54b7c0d254620e3 100644
--- a/src/isdb/MetainferenceBase.h
+++ b/src/isdb/MetainferenceBase.h
@@ -25,7 +25,9 @@
#include "core/ActionWithValue.h"
#include "core/ActionAtomistic.h"
#include "core/ActionWithArguments.h"
+#include "core/PlumedMain.h"
#include "tools/Random.h"
+#include "tools/OpenMP.h"
#define PLUMED_METAINF_INIT(ao) Action(ao),MetainferenceBase(ao)
@@ -277,7 +279,7 @@ void MetainferenceBase::setDerivatives() {
// Resize all derivative arrays
forces.resize( nder ); forcesToApply.resize( nder );
- for(unsigned i=0; i<getNumberOfComponents(); ++i) getPntrToComponent(i)->resizeDerivatives(nder);
+ for(int i=0; i<getNumberOfComponents(); ++i) getPntrToComponent(i)->resizeDerivatives(nder);
}
inline
@@ -312,11 +314,11 @@ void MetainferenceBase::calculateNumericalDerivatives( ActionWithValue* a ) {
}
if( getNumberOfAtoms()>0 ) {
Matrix<double> save_derivatives( getNumberOfComponents(), getNumberOfArguments() );
- for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+ for(int j=0; j<getNumberOfComponents(); ++j) {
for(unsigned i=0; i<getNumberOfArguments(); ++i) if(getPntrToComponent(j)->hasDerivatives()) save_derivatives(j,i)=getPntrToComponent(j)->getDerivative(i);
}
calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );
- for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+ for(int j=0; j<getNumberOfComponents(); ++j) {
for(unsigned i=0; i<getNumberOfArguments(); ++i) if(getPntrToComponent(j)->hasDerivatives()) getPntrToComponent(j)->addDerivative( i, save_derivatives(j,i) );
}
}
@@ -325,7 +327,7 @@ void MetainferenceBase::calculateNumericalDerivatives( ActionWithValue* a ) {
inline
void MetainferenceBase::apply() {
bool wasforced=false; forcesToApply.assign(forcesToApply.size(),0.0);
- for(unsigned i=0; i<getNumberOfComponents(); ++i) {
+ for(int i=0; i<getNumberOfComponents(); ++i) {
if( getPntrToComponent(i)->applyForce( forces ) ) {
wasforced=true;
for(unsigned i=0; i<forces.size(); ++i) forcesToApply[i]+=forces[i];
diff --git a/src/isdb/NOE.cpp b/src/isdb/NOE.cpp
index 52f386813723b1d802ccc283d7cf1a863e9a25b1..02a10de1c3c002af76acdfb5dae27c037c411f7e 100644
--- a/src/isdb/NOE.cpp
+++ b/src/isdb/NOE.cpp
@@ -22,7 +22,6 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
#include "tools/NeighborList.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include <string>
@@ -165,6 +164,8 @@ NOE::NOE(const ActionOptions&ao):
if(pbc) log.printf(" using periodic boundary conditions\n");
else log.printf(" without periodic boundary conditions\n");
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
if(!getDoScore()) {
for(unsigned i=0; i<nga.size(); i++) {
string num; Tools::convert(i,num);
@@ -215,7 +216,6 @@ void NOE::calculate()
double noe=0;
unsigned index=0;
for(unsigned k=0; k<i; k++) index+=nga[k];
- const double c_aver=1./static_cast<double>(nga[i]);
string num; Tools::convert(i,num);
Value* val=getPntrToComponent("noe_"+num);
// cycle over equivalent atoms
@@ -230,11 +230,9 @@ void NOE::calculate()
const double ir2=1./distance.modulo2();
const double ir6=ir2*ir2*ir2;
const double ir8=6*ir6*ir2;
- const double tmpir6=c_aver*ir6;
- const double tmpir8=c_aver*ir8;
- noe += tmpir6;
- deriv[index+j] = tmpir8*distance;
+ noe += ir6;
+ deriv[index+j] = ir8*distance;
if(!getDoScore()) {
dervir += Tensor(distance, deriv[index+j]);
setAtomsDerivatives(val, i0, deriv[index+j]);
diff --git a/src/isdb/PRE.cpp b/src/isdb/PRE.cpp
index a5d806ed93573de809a34716ae93ea28e0ef13d9..afc25e293f45198cf2115500f1854970a784b6d1 100644
--- a/src/isdb/PRE.cpp
+++ b/src/isdb/PRE.cpp
@@ -22,7 +22,6 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
#include "tools/NeighborList.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include <string>
@@ -205,6 +204,8 @@ PRE::PRE(const ActionOptions&ao):
if(pbc) log.printf(" using periodic boundary conditions\n");
else log.printf(" without periodic boundary conditions\n");
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
if(!getDoScore()) {
for(unsigned i=0; i<nga.size(); i++) {
string num; Tools::convert(i,num);
diff --git a/src/isdb/RDC.cpp b/src/isdb/RDC.cpp
index 8827c8d388cb2a8d7ade0356c222fd57a1020b15..a0be6cf1992674aaf188e64c3a6b4e05aac974d5 100644
--- a/src/isdb/RDC.cpp
+++ b/src/isdb/RDC.cpp
@@ -21,8 +21,6 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#ifdef __PLUMED_HAS_GSL
@@ -228,10 +226,9 @@ RDC::RDC(const ActionOptions&ao):
const double RDCConst = 0.3356806;
const double PCSConst = 1.0;
- bool rdc = true;
- if( getName().find("RDC")!=std::string::npos) { Const *= RDCConst; rdc=true;}
- else if( getName().find("PCS")!=std::string::npos) { Const *= PCSConst; rdc=false;}
+ if( getName().find("RDC")!=std::string::npos) { Const *= RDCConst; }
+ else if( getName().find("PCS")!=std::string::npos) { Const *= PCSConst; }
// Read in the atoms
vector<AtomNumber> t, atoms;
@@ -288,7 +285,9 @@ RDC::RDC(const ActionOptions&ao):
log<<" Bibliography "
<<plumed.cite("Camilloni C, Vendruscolo M, J. Phys. Chem. B 119, 653 (2015)")
- <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)") <<"\n";
+ <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)");
+ log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
if(!getDoScore()&&!svd) {
for(unsigned i=0; i<ndata; i++) {
diff --git a/src/isdb/Rescale.cpp b/src/isdb/Rescale.cpp
index 3707c1c2217c8e4ee1124f2fe35e33d900702da0..f28dce8b53106f3b4a384c16f6c5e9fb53cea03d 100644
--- a/src/isdb/Rescale.cpp
+++ b/src/isdb/Rescale.cpp
@@ -288,6 +288,9 @@ Rescale::Rescale(const ActionOptions&ao):
log.printf(" do MC every %d steps\n", MCstride_);
log.printf("\n");
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
+
// add components
addComponent("igamma"); componentIsNotPeriodic("igamma");
addComponent("accgamma"); componentIsNotPeriodic("accgamma");
diff --git a/src/isdb/SAXS.cpp b/src/isdb/SAXS.cpp
index 3f5ab61dcfc856521d64ccaf423901a9233950d8..2e965236b7b723c4634b689317a0138553b7b50d 100644
--- a/src/isdb/SAXS.cpp
+++ b/src/isdb/SAXS.cpp
@@ -27,10 +27,8 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
#include "core/ActionSet.h"
-#include "core/PlumedMain.h"
#include "core/SetupMolInfo.h"
#include "tools/Communicator.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include <string>
@@ -277,6 +275,7 @@ SAXS::SAXS(const ActionOptions&ao):
log<<plumed.cite("Fraser, MacRae, Suzuki, J. Appl. Crystallogr., 11, 693–694 (1978).");
log<<plumed.cite("Brown, Fox, Maslen, O'Keefe, Willis, International Tables for Crystallography C, 554–595 (International Union of Crystallography, 2006).");
}
+ log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
requestAtoms(atoms);
diff --git a/src/isdb/Select.cpp b/src/isdb/Select.cpp
index de6f0ae4b11fd99e3d185df411faa66242d64c46..14368243a5f7f1540deecd7350560e758e78238a 100644
--- a/src/isdb/Select.cpp
+++ b/src/isdb/Select.cpp
@@ -95,6 +95,8 @@ Select::Select(const ActionOptions&ao):
checkRead();
log.printf(" select based on %s\n",selector_.c_str());
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
}
void Select::calculate()
diff --git a/src/lib/Makefile b/src/lib/Makefile
index f77e40c3ae89221d48d4137de2de047fcdb992c8..340ef0b81141afdf3cff8a9b23fd855ada6e8664 100644
--- a/src/lib/Makefile
+++ b/src/lib/Makefile
@@ -94,7 +94,7 @@ install-build:
mkdir -p install/
$(MAKE) PLUMED_INSTALL=Install all
ifdef LD_RO
- $(MAKE) install/kernel.o
+ $(MAKE) PLUMED_INSTALL=Install install/kernel.o
endif
# modulefile
@cat modulefile.in | \
@@ -222,14 +222,19 @@ endif
ifdef LD_RO
cp install/kernel.o "$(DESTDIR)$(libdir)/$(program_name)/obj/kernel.o"
else
- ../maketools/copyobjects "$(DESTDIR)$(libdir)/$(program_name)/obj/k" $(OBJ_KERNEL)
+ ../maketools/copyobjects "$(DESTDIR)$(libdir)/$(program_name)/obj/k" $(subst ../config/Config.o,../config/ConfigInstall.o,$(OBJ_KERNEL))
endif
cp $(OBJ_WRAPPER) "$(DESTDIR)$(libdir)/$(program_name)/obj/PlumedStatic.o"
cp $(OBJ_DYNAMIC_WRAPPER) "$(DESTDIR)$(libdir)/$(program_name)/obj/Plumed.o"
# also copy .h files into include/ dir
cd ../../src ; tar cf - */*.h */*/*.h | tar xf - -C "$(DESTDIR)$(includedir)/$(program_name)/"
# install executable
+# for OSX we can use the dynamically linked executable
+ifeq ($(SOEXT),dylib)
+ cp install/plumed-shared "$(DESTDIR)$(bindir)/$(program_name)"
+else
cp install/plumed "$(DESTDIR)$(bindir)/$(program_name)"
+endif
# patch file for cross compiling
cp install/plumed-patch "$(DESTDIR)$(bindir)/$(program_name)-patch"
# config file for cross compiling
@@ -243,10 +248,6 @@ endif
ifdef SOEXT
cp install/libplumed.$(SOEXT) "$(DESTDIR)$(libdir)/lib$(program_name).$(SOEXT)"
cp install/libplumedKernel.$(SOEXT) "$(DESTDIR)$(libdir)/lib$(program_name)Kernel.$(SOEXT)"
-ifeq ($(SOEXT),dylib)
- install_name_tool -id "$(libdir)/lib$(program_name).$(SOEXT)" "$(DESTDIR)$(libdir)/lib$(program_name).$(SOEXT)"
- install_name_tool -id "$(libdir)/lib$(program_name)Kernel.$(SOEXT)" "$(DESTDIR)$(libdir)/lib$(program_name)Kernel.$(SOEXT)"
-endif
endif
ifdef AR_CR
cp install/libplumedWrapper.a "$(DESTDIR)$(libdir)/lib$(program_name)Wrapper.a"
@@ -405,21 +406,32 @@ $(PLUMED_KERNEL):$(OBJ_KERNEL)
ifeq ($(PLUMED_INSTALL),Install)
mkdir -p install
cd install && $(LDSHARED) -o libplumedKernel.$(SOEXT) $(addprefix ../,$(OBJ_KERNEL)) $(DYNAMIC_LIBS)
+ifeq ($(SOEXT),dylib)
+ install_name_tool -id "$(libdir)/lib$(program_name)Kernel.$(SOEXT)" $@
+endif
else
$(LDSHARED) -o $@ $^ $(DYNAMIC_LIBS)
ifeq ($(SOEXT),dylib)
- install_name_tool -id "$(realpath .)/libplumedKernel.$(SOEXT)" libplumedKernel.$(SOEXT)
+ install_name_tool -id "$(realpath .)/libplumedKernel.$(SOEXT)" $@
endif
endif
-$(PLUMED_SHARED_OBJ): $(OBJ_KERNEL) $(OBJ_WRAPPER)
+# dependence on PLUMED_KERNEL is required for build on OSX to work correctly:
+$(PLUMED_SHARED_OBJ): $(OBJ_KERNEL) $(OBJ_WRAPPER) $(PLUMED_KERNEL)
ifeq ($(PLUMED_INSTALL),Install)
mkdir -p install
+ifeq ($(SOEXT),dylib)
+ cd install && $(LDSHARED) -o libplumed.$(SOEXT) libplumedKernel.dylib $(addprefix ../,$(OBJ_WRAPPER)) $(LIBS)
+ install_name_tool -id "$(libdir)/lib$(program_name).$(SOEXT)" $@
+else
cd install && $(LDSHARED) -o libplumed.$(SOEXT) $(addprefix ../,$(OBJ_KERNEL)) $(addprefix ../,$(OBJ_WRAPPER)) $(DYNAMIC_LIBS)
+endif
else
- $(LDSHARED) -o $@ $^ $(DYNAMIC_LIBS)
ifeq ($(SOEXT),dylib)
+ $(LDSHARED) -o $@ $(OBJ_WRAPPER) libplumedKernel.dylib $(LIBS)
install_name_tool -id "$(realpath .)/libplumed.$(SOEXT)" $@
+else
+ $(LDSHARED) -o $@ $(OBJ_KERNEL) $(OBJ_WRAPPER) $(DYNAMIC_LIBS)
endif
endif
@@ -537,8 +549,7 @@ endif
.PHONY: clean dirslinks
clean:
rm -f $(CLEANLIST)
- rm -f $(PLUMED_MAIN_STATIC) $(PLUMED_MAIN_SHARED) $(PLUMED_MAIN_RUNTIME)
- rm -f Plumed.inc* plumed-* Plumed.cmake*
+ rm -f plumed Plumed.inc* plumed-* Plumed.cmake*
# this is not necessary, I leave it here to remove spurious plumed.vim files generated with
# the first version of plumed.vim syntax file:
rm -f plumed.vim
diff --git a/src/maketools/codecheck b/src/maketools/codecheck
index 4c59c8349bb8cf24a6998d4db4f84fcb0541c059..04db28d03920c8d7f9f980670630ba203faed513 100755
--- a/src/maketools/codecheck
+++ b/src/maketools/codecheck
@@ -52,7 +52,7 @@ fi
# done
# echo "+++++++++++++++++++++++++++++++++++++"
-TMPDIR="$(mktemp -d)"
+TMPDIR="$(mktemp -dt plumed.XXXXXX)"
FATAL_FILE="$TMPDIR/codecheck.fatal"
CLEAN_FILE="$TMPDIR/codecheck.clean"
diff --git a/src/maketools/plumedcheck b/src/maketools/plumedcheck
index 9f0b038cbf1214744f37e3340f802ce8a84b5733..6d442b6b5fb7de3f8369a50777655e4fbff3776b 100755
--- a/src/maketools/plumedcheck
+++ b/src/maketools/plumedcheck
@@ -14,7 +14,7 @@
# DOC: In case you think you have a valid reason for a code not passing the check
# DOC: to be merged, please contact the developers.
-TEMP=$(mktemp)
+TEMP=$(mktemp -t plumed.XXXXXX)
cat > $TEMP << \EOF
@@ -144,7 +144,7 @@ BEGIN{
core_modules["reference"]=1
# create tmp dir for future usage
- "mktemp -d" | getline tmpdir
+ "mktemp -dt plumed.XXXXXX" | getline tmpdir
}
# for each input file
diff --git a/src/maketools/update-config-txt.sh b/src/maketools/update-config-txt.sh
index 4025222da3c22791b0a07a7be46dc8404f4b39c2..6db9cb1588667bf77a53e1f37a0fcc89c360a5c9 100755
--- a/src/maketools/update-config-txt.sh
+++ b/src/maketools/update-config-txt.sh
@@ -101,7 +101,14 @@ echo "# version strings"
echo "# syntax: version short/long/git number"
echo "$version"
echo
+echo "# python executable"
+echo "# syntax: python_bin executable"
+echo "# empty string means that python has not been configured"
echo "python_bin $python_bin"
+echo
+echo "# command to lauch mpi processes"
+echo "# syntax: mpiexec command"
+echo "# empty string means that mpiexec was not chosen at configure time"
echo "mpiexec $mpiexec"
echo
echo "# list of 'has' options"
diff --git a/src/mapping/Mapping.cpp b/src/mapping/Mapping.cpp
index c0006dd684561db7d08e5eaa9e97e7b708ece91d..5f069e6ef15c39b93f8a9f96f67e2ed8ed171360 100644
--- a/src/mapping/Mapping.cpp
+++ b/src/mapping/Mapping.cpp
@@ -56,7 +56,7 @@ Mapping::Mapping(const ActionOptions&ao):
std::string mtype; parse("TYPE",mtype);
bool skipchecks; parseFlag("DISABLE_CHECKS",skipchecks);
// Setup the object that does the mapping
- mymap = new PointWiseMapping( mtype, skipchecks );
+ mymap.reset( new PointWiseMapping( mtype, skipchecks ) );
// Read the properties we require
if( keywords.exists("PROPERTY") ) {
@@ -124,10 +124,6 @@ void Mapping::turnOnDerivatives() {
needsDerivatives();
}
-Mapping::~Mapping() {
- delete mymap;
-}
-
void Mapping::prepare() {
if( mymap->mappingNeedsSetup() ) {
// Get the arguments and atoms that are required
@@ -208,11 +204,11 @@ void Mapping::calculateNumericalDerivatives( ActionWithValue* a ) {
}
if( getNumberOfAtoms()>0 ) {
Matrix<double> save_derivatives( getNumberOfComponents(), getNumberOfArguments() );
- for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+ for(int j=0; j<getNumberOfComponents(); ++j) {
for(unsigned i=0; i<getNumberOfArguments(); ++i) save_derivatives(j,i)=getPntrToComponent(j)->getDerivative(i);
}
calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );
- for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+ for(int j=0; j<getNumberOfComponents(); ++j) {
for(unsigned i=0; i<getNumberOfArguments(); ++i) getPntrToComponent(j)->addDerivative( i, save_derivatives(j,i) );
}
}
diff --git a/src/mapping/Mapping.h b/src/mapping/Mapping.h
index 1fea8be58b3f94077066d17fd7f7b4abfb212b44..aa6143ca1ff862b1ad07e320b050e7a44a03af24 100644
--- a/src/mapping/Mapping.h
+++ b/src/mapping/Mapping.h
@@ -28,6 +28,7 @@
#include "vesselbase/ActionWithVessel.h"
#include "reference/PointWiseMapping.h"
#include <vector>
+#include <memory>
namespace PLMD {
@@ -46,7 +47,7 @@ private:
// The derivative wrt to the distance from the frame
std::vector<double> dfframes;
/// This holds all the reference information
- PointWiseMapping* mymap;
+ std::unique_ptr<PointWiseMapping> mymap;
/// The forces on each of the derivatives (used in apply)
std::vector<double> forcesToApply;
protected:
@@ -69,7 +70,6 @@ protected:
public:
static void registerKeywords( Keywords& keys );
explicit Mapping(const ActionOptions&);
- ~Mapping();
/// Overload the virtual functions that appear in both ActionAtomistic and ActionWithArguments
void turnOnDerivatives();
void calculateNumericalDerivatives( ActionWithValue* a=NULL );
diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index 02d7c4776053dfd682d4755933a35d5db3368afd..2eef570d057d27e2774ebae5f0ca704543f88430 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -176,7 +176,7 @@ private:
MultiValue myvals;
ReferenceValuePack mypack;
/// The position of the reference configuration (the one we align to)
- ReferenceConfiguration* myref;
+ std::unique_ptr<ReferenceConfiguration> myref;
/// The eigenvectors we are interested in
std::vector<Direction> directions;
/// Stuff for applying forces
@@ -184,7 +184,6 @@ private:
public:
static void registerKeywords( Keywords& keys );
explicit PCAVars(const ActionOptions&);
- ~PCAVars();
unsigned getNumberOfDerivatives();
void lockRequests();
void unlockRequests();
@@ -239,8 +238,8 @@ PCAVars::PCAVars(const ActionOptions& ao):
expandArgKeywordInPDB( mypdb );
if(do_read) {
if( nfram==0 ) {
- myref = metricRegister().create<ReferenceConfiguration>( mtype, mypdb );
- Direction* tdir = dynamic_cast<Direction*>( myref );
+ myref.reset( metricRegister().create<ReferenceConfiguration>( mtype, mypdb ) );
+ Direction* tdir = dynamic_cast<Direction*>( myref.get() );
if( tdir ) error("first frame should be reference configuration - not direction of vector");
if( !myref->pcaIsEnabledForThisReference() ) error("can't do PCA with reference type " + mtype );
std::vector<std::string> remarks( mypdb.getRemark() ); std::string rtype;
@@ -308,11 +307,7 @@ PCAVars::PCAVars(const ActionOptions& ao):
// Resize all derivative arrays
forces.resize( nder ); forcesToApply.resize( nder );
- for(unsigned i=0; i<getNumberOfComponents(); ++i) getPntrToComponent(i)->resizeDerivatives(nder);
-}
-
-PCAVars::~PCAVars() {
- delete myref;
+ for(int i=0; i<getNumberOfComponents(); ++i) getPntrToComponent(i)->resizeDerivatives(nder);
}
unsigned PCAVars::getNumberOfDerivatives() {
@@ -350,7 +345,7 @@ void PCAVars::calculate() {
// Now calculate projections on pca vectors
Vector adif, ader; Tensor fvir, tvir;
- for(unsigned i=0; i<getNumberOfComponents()-1; ++i) { // One less component as we also have residual
+ for(int i=0; i<getNumberOfComponents()-1; ++i) { // One less component as we also have residual
double proj=myref->projectDisplacementOnVector( directions[i], getArguments(), args, mypack );
// And now accumulate derivatives
Value* eid=getPntrToComponent(i);
@@ -406,11 +401,11 @@ void PCAVars::calculateNumericalDerivatives( ActionWithValue* a ) {
}
if( getNumberOfAtoms()>0 ) {
Matrix<double> save_derivatives( getNumberOfComponents(), getNumberOfArguments() );
- for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+ for(int j=0; j<getNumberOfComponents(); ++j) {
for(unsigned i=0; i<getNumberOfArguments(); ++i) save_derivatives(j,i)=getPntrToComponent(j)->getDerivative(i);
}
calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );
- for(unsigned j=0; j<getNumberOfComponents(); ++j) {
+ for(int j=0; j<getNumberOfComponents(); ++j) {
for(unsigned i=0; i<getNumberOfArguments(); ++i) getPntrToComponent(j)->addDerivative( i, save_derivatives(j,i) );
}
}
@@ -419,7 +414,7 @@ void PCAVars::calculateNumericalDerivatives( ActionWithValue* a ) {
void PCAVars::apply() {
bool wasforced=false; forcesToApply.assign(forcesToApply.size(),0.0);
- for(unsigned i=0; i<getNumberOfComponents(); ++i) {
+ for(int i=0; i<getNumberOfComponents(); ++i) {
if( getPntrToComponent(i)->applyForce( forces ) ) {
wasforced=true;
for(unsigned i=0; i<forces.size(); ++i) forcesToApply[i]+=forces[i];
diff --git a/src/mapping/PathTools.cpp b/src/mapping/PathTools.cpp
index b10e3d8a8be38d9e0fb03409f1021faaaac075f6..c3bd8a2e47fe3721a3e8d49c294673b1b6f31d13 100644
--- a/src/mapping/PathTools.cpp
+++ b/src/mapping/PathTools.cpp
@@ -207,14 +207,14 @@ int PathTools::main(FILE* in, FILE*out,Communicator& pc) {
std::string istart; parse("--start",istart); FILE* fp2=fopen(istart.c_str(),"r"); PDB mystartpdb;
if( istart.length()==0 ) error("input is missing use --istart + --iend or --path");
if( !mystartpdb.readFromFilepointer(fp2,false,0.1) ) error("could not read fila " + istart);
- ReferenceConfiguration* sframe=metricRegister().create<ReferenceConfiguration>( mtype, mystartpdb );
+ std::unique_ptr<ReferenceConfiguration> sframe( metricRegister().create<ReferenceConfiguration>( mtype, mystartpdb ) );
fclose(fp2);
// Read final frame
std::string iend; parse("--end",iend); FILE* fp1=fopen(iend.c_str(),"r"); PDB myendpdb;
if( iend.length()==0 ) error("input is missing using --istart + --iend or --path");
if( !myendpdb.readFromFilepointer(fp1,false,0.1) ) error("could not read fila " + iend);
- ReferenceConfiguration* eframe=metricRegister().create<ReferenceConfiguration>( mtype, myendpdb );
+ std::unique_ptr<ReferenceConfiguration> eframe( metricRegister().create<ReferenceConfiguration>( mtype, myendpdb ) );
fclose(fp1);
// Get atoms and arg requests
@@ -286,7 +286,7 @@ int PathTools::main(FILE* in, FILE*out,Communicator& pc) {
for(unsigned i=0; i<final_path.size(); ++i) { final_path[i]->print( ofile, ofmt, 10. ); delete final_path[i]; }
// Delete the args as we don't need them anymore
for(unsigned i=0; i<args.size(); ++i) delete args[i];
- ofile.close(); delete sframe; delete eframe; return 0;
+ ofile.close(); return 0;
}
} // End of namespace
diff --git a/src/multicolvar/AlphaBeta.cpp b/src/multicolvar/AlphaBeta.cpp
index aea79fc2ea288a922e5897281e718f759902cfc1..2d7e787ef6c757e307065ce21a5870007e4700e7 100644
--- a/src/multicolvar/AlphaBeta.cpp
+++ b/src/multicolvar/AlphaBeta.cpp
@@ -96,6 +96,7 @@ Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle o
class AlphaBeta : public MultiColvarBase {
private:
std::vector<double> target;
+ std::vector<double> coefficient;
public:
static void registerKeywords( Keywords& keys );
explicit AlphaBeta(const ActionOptions&);
@@ -115,7 +116,10 @@ void AlphaBeta::registerKeywords( Keywords& keys ) {
keys.reset_style("ATOMS","atoms");
keys.add("numbered","REFERENCE","the reference values for each of the torsional angles. If you use a single REFERENCE value the "
"same reference value is used for all torsions");
+ keys.add("numbered","COEFFICIENT","the coefficient for each of the torsional angles. If you use a single COEFFICIENT value the "
+ "same reference value is used for all torsions");
keys.reset_style("REFERENCE","compulsory");
+ keys.reset_style("COEFFICIENT","optional");
}
AlphaBeta::AlphaBeta(const ActionOptions&ao):
@@ -128,6 +132,8 @@ AlphaBeta::AlphaBeta(const ActionOptions&ao):
setupMultiColvarBase( all_atoms );
// Resize target
target.resize( getFullNumberOfTasks() );
+ // Resize coeff
+ coefficient.resize( getFullNumberOfTasks(), 1.0);
// Setup central atom indices
std::vector<bool> catom_ind(4, false);
catom_ind[1]=catom_ind[2]=true;
@@ -146,6 +152,19 @@ AlphaBeta::AlphaBeta(const ActionOptions&ao):
error("found wrong number of REFERENCE values");
}
+ // Read in reference values
+ unsigned ncoefficient=0;
+ for(unsigned i=0; i<coefficient.size(); ++i) {
+ if( !parseNumbered( "COEFFICIENT", i+1, coefficient[i] ) ) break;
+ ncoefficient++;
+ }
+ if( ncoefficient==0 ) {
+ parse("COEFFICIENT",coefficient[0]);
+ for(unsigned i=1; i<coefficient.size(); ++i) coefficient[i]=coefficient[0];
+ } else if( ncoefficient !=coefficient.size() ) {
+ error("found wrong number of COEFFICIENT values");
+ }
+
// And setup the ActionWithVessel
if( getNumberOfVessels()==0 ) {
std::string fake_input;
@@ -165,8 +184,8 @@ double AlphaBeta::compute( const unsigned& tindex, AtomValuePack& myatoms ) cons
Vector dd0,dd1,dd2;
PLMD::Torsion t;
const double value = t.compute(d0,d1,d2,dd0,dd1,dd2);
- const double svalue = -0.5*sin(value-target[tindex]);
- const double cvalue = 1.+cos(value-target[tindex]);
+ const double svalue = -0.5*coefficient[tindex]*sin(value-target[tindex]);
+ const double cvalue = coefficient[tindex]*(1.+cos(value-target[tindex]));
dd0 *= svalue;
dd1 *= svalue;
diff --git a/src/multicolvar/VolumeBetweenContours.cpp b/src/multicolvar/VolumeBetweenContours.cpp
index 737c77ffca2bd3ed681faf0be18461e7591cf897..d1e1bfcd00b8aa733de52b4adf26242bf567fd0f 100644
--- a/src/multicolvar/VolumeBetweenContours.cpp
+++ b/src/multicolvar/VolumeBetweenContours.cpp
@@ -24,6 +24,7 @@
#include "tools/KernelFunctions.h"
#include "tools/SwitchingFunction.h"
#include "ActionVolume.h"
+#include <memory>
//+PLUMEDOC VOLUMES INENVELOPE
/*
@@ -63,7 +64,7 @@ namespace multicolvar {
class VolumeInEnvelope : public ActionVolume {
private:
LinkCells mylinks;
- KernelFunctions* kernel;
+ std::unique_ptr<KernelFunctions> kernel;
std::vector<Value*> pos;
std::vector<Vector> ltmp_pos;
std::vector<unsigned> ltmp_ind;
@@ -104,7 +105,7 @@ VolumeInEnvelope::VolumeInEnvelope(const ActionOptions& ao):
std::vector<double> pp(3,0.0), bandwidth(3); parseVector("BANDWIDTH",bandwidth);
log.printf(" using %s kernel with bandwidths %f %f %f \n",getKernelType().c_str(),bandwidth[0],bandwidth[1],bandwidth[2] );
- kernel = new KernelFunctions( pp, bandwidth, getKernelType(), "DIAGONAL", 1.0 );
+ kernel.reset( new KernelFunctions( pp, bandwidth, getKernelType(), "DIAGONAL", 1.0 ) );
for(unsigned i=0; i<3; ++i) { pos.push_back(new Value()); pos[i]->setNotPeriodic(); }
std::vector<double> csupport( kernel->getContinuousSupport() );
double maxs = csupport[0];
@@ -115,7 +116,7 @@ VolumeInEnvelope::VolumeInEnvelope(const ActionOptions& ao):
}
VolumeInEnvelope::~VolumeInEnvelope() {
- delete kernel; for(unsigned j=0; j<3; ++j) delete pos[j];
+ for(unsigned j=0; j<3; ++j) delete pos[j];
}
void VolumeInEnvelope::setupRegions() {
diff --git a/src/multicolvar/VolumeGradientBase.h b/src/multicolvar/VolumeGradientBase.h
index 4a92757fc487a753983de5791738a2f02926a750..22d8ff8ad054b17fe9a2b8a5940ec10072de7c41 100644
--- a/src/multicolvar/VolumeGradientBase.h
+++ b/src/multicolvar/VolumeGradientBase.h
@@ -81,7 +81,7 @@ Vector VolumeGradientBase::getPosition( int iatom ) const {
// This is for numerical derivatives of quantity wrt to the local atoms
Vector tmp_p = ActionAtomistic::getPosition(iatom);
if( bridgeVariable<3*getNumberOfAtoms() ) {
- if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
+ if( static_cast<int>(bridgeVariable)>=3*iatom && static_cast<int>(bridgeVariable)<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
}
// This makes sure that numerical derivatives of virial are calculated correctly
tmp_p = ActionAtomistic::getPbc().realToScaled( tmp_p );
diff --git a/src/pamm/PammObject.cpp b/src/pamm/PammObject.cpp
index 54430672297d8d6c09ded516a7652f4f1f86e733..7606d7f1beb50aba419b216a9f55fccc7a1e4be2 100644
--- a/src/pamm/PammObject.cpp
+++ b/src/pamm/PammObject.cpp
@@ -21,6 +21,7 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "PammObject.h"
#include "tools/IFile.h"
+#include <memory>
namespace PLMD {
namespace pamm {
@@ -65,10 +66,11 @@ void PammObject::setup( const std::string& filename, const double& reg, const st
ifile.open(filename); ifile.allowIgnoredFields(); kernels.resize(0);
for(unsigned k=0;; ++k) {
- KernelFunctions* kk = KernelFunctions::read( &ifile, false, valnames );
+ std::unique_ptr<KernelFunctions> kk = KernelFunctions::read( &ifile, false, valnames );
if( !kk ) break ;
kk->normalize( pos );
- kernels.push_back( kk );
+ kernels.push_back( kk.release() ); // kernels should be changed into a vector<unique_ptr>.
+ // meanwhile, I just release the unique_ptr herelease the unique_ptr here. GB
ifile.scanField();
}
ifile.close();
diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp
index 337fcdfe8afb934679a1daf084f1b20214d77995..643f4cb5e24068a7604c8f70866d2d5706412092 100644
--- a/src/secondarystructure/AlphaRMSD.cpp
+++ b/src/secondarystructure/AlphaRMSD.cpp
@@ -70,7 +70,15 @@ protein that are in an alpha helical configuration.
\plumedfile
MOLINFO STRUCTURE=helix.pdb
-ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
+hh: ALPHARMSD RESIDUES=all
+\endplumedfile
+
+Here the same is done use RMSD instead of DRMSD
+
+\plumedfile
+MOLINFO STRUCTURE=helix.pdb
+WHOLEMOLECULES ENTITY0=1-100
+hh: ALPHARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1
\endplumedfile
*/
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index 780e378bc183db5b68d9b11b7d13f9299a3c24cb..fe843bd755b33a719a11f37301aba1153a075c46 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -71,10 +71,17 @@ The following input calculates the number of six residue segments of
protein that are in an antiparallel beta sheet configuration.
\plumedfile
-MOLINFO STRUCTURE=helix.pdb
-ANTIBETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
+MOLINFO STRUCTURE=beta.pdb
+ab: ANTIBETARMSD RESIDUES=all STRANDS_CUTOFF=1
\endplumedfile
+Here the same is done use RMSD instead of DRMSD
+
+\plumedfile
+MOLINFO STRUCTURE=helix.pdb
+WHOLEMOLECULES ENTITY0=1-100
+hh: ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1 STRANDS_CUTOFF=1
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index c28bee1f1f7c563130274130d0dfc7c352fd7a67..4329edd6ee6e70ca9886796536c4b04e0a6ccfe6 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -70,9 +70,17 @@ anthing other than TYPE=DRMSD. For more details as to how to do this see \ref W
The following input calculates the number of six residue segments of
protein that are in an parallel beta sheet configuration.
+\plumedfile
+MOLINFO STRUCTURE=beta.pdb
+pb: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1
+\endplumedfile
+
+Here the same is done use RMSD instead of DRMSD
+
\plumedfile
MOLINFO STRUCTURE=helix.pdb
-PARABETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
+WHOLEMOLECULES ENTITY0=1-100
+hh: PARABETARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1 STRANDS_CUTOFF=1
\endplumedfile
*/
diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp
index 21a4911b2281c2848322ba6b23090c3ebb77b855..2ddd5b296d1b84d17925719156b1dbb089164445 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.cpp
+++ b/src/secondarystructure/SecondaryStructureRMSD.cpp
@@ -45,7 +45,7 @@ void SecondaryStructureRMSD::registerKeywords( Keywords& keys ) {
keys.add("compulsory","TYPE","DRMSD","the manner in which RMSD alignment is performed. Should be OPTIMAL, SIMPLE or DRMSD. "
"For more details on the OPTIMAL and SIMPLE methods see \\ref RMSD. For more details on the "
"DRMSD method see \\ref DRMSD.");
- keys.add("compulsory","R_0","The r_0 parameter of the switching function.");
+ keys.add("compulsory","R_0","0.08","The r_0 parameter of the switching function.");
keys.add("compulsory","D_0","0.0","The d_0 parameter of the switching function");
keys.add("compulsory","NN","8","The n parameter of the switching function");
keys.add("compulsory","MM","12","The m parameter of the switching function");
@@ -112,7 +112,8 @@ void SecondaryStructureRMSD::readBackboneAtoms( const std::string& moltype, std:
std::vector<std::string> resstrings; parseVector( "RESIDUES", resstrings );
if( !verbose_output ) {
- if(resstrings[0]=="all") {
+ if(resstrings.size()==0) error("residues are not defined, check the keyword RESIDUES");
+ else if(resstrings[0]=="all") {
log.printf(" examining all possible secondary structure combinations\n");
} else {
log.printf(" examining secondary structure in residue positions : %s \n",resstrings[0].c_str() );
diff --git a/src/tools/BiasRepresentation.cpp b/src/tools/BiasRepresentation.cpp
index c81524de749babb92f54e757c1b2d15a2053d7c5..bafae408da3afbd2642e5d826114955cf795ae42 100644
--- a/src/tools/BiasRepresentation.cpp
+++ b/src/tools/BiasRepresentation.cpp
@@ -115,24 +115,24 @@ Value* BiasRepresentation::getPtrToValue(unsigned i) {
return values[i];
}
-KernelFunctions* BiasRepresentation::readFromPoint(IFile *ifile) {
+std::unique_ptr<KernelFunctions> BiasRepresentation::readFromPoint(IFile *ifile) {
vector<double> cc( names.size() );
for(unsigned i=0; i<names.size(); ++i) {
ifile->scanField(names[i],cc[i]);
}
double h=1.0;
- return new KernelFunctions(cc,histosigma,"gaussian","DIAGONAL",h);
+ return std::unique_ptr<KernelFunctions>( new KernelFunctions(cc,histosigma,"gaussian","DIAGONAL",h) );
}
void BiasRepresentation::pushKernel( IFile *ifile ) {
std::unique_ptr<KernelFunctions> kk;
// here below the reading of the kernel is completely hidden
if(histosigma.size()==0) {
ifile->allowIgnoredFields();
- kk.reset(KernelFunctions::read(ifile,true,names));
+ kk=KernelFunctions::read(ifile,true,names);
} else {
// when doing histogram assume gaussian with a given diagonal sigma
// and neglect all the rest
- kk.reset(readFromPoint(ifile));
+ kk=readFromPoint(ifile);
}
// the bias factor is not something about the kernels but
// must be stored to keep the bias/free energy duality
diff --git a/src/tools/BiasRepresentation.h b/src/tools/BiasRepresentation.h
index a775a0120cdc6bde5327121529c0a060e65bf880..93c613a34654370300eee16171daffaf76669bcb 100644
--- a/src/tools/BiasRepresentation.h
+++ b/src/tools/BiasRepresentation.h
@@ -76,7 +76,7 @@ public:
/// get the pointer to the grid
Grid* getGridPtr();
/// get a new histogram point from a file
- KernelFunctions* readFromPoint(IFile *ifile);
+ std::unique_ptr<KernelFunctions> readFromPoint(IFile *ifile);
/// get an automatic min/max from the set so to know how to configure the grid
void getMinMaxBin(std::vector<double> &vmin, std::vector<double> &vmax, std::vector<unsigned> &vbin);
/// clear the representation (grid included)
diff --git a/src/tools/Exception.cpp b/src/tools/Exception.cpp
index 6982d6683caf4a5686d2aa36f1073f9503906f55..0e05fb66b4497f6a8d673b7d0dd9e94b53c06b1d 100644
--- a/src/tools/Exception.cpp
+++ b/src/tools/Exception.cpp
@@ -49,7 +49,7 @@ std::string Exception::trace() {
std::string Exception::format(const std::string&msg,const std::string&file,unsigned line,const std::string&function) {
std::string message;
if(getenv("PLUMED_STACK_TRACE"))message+=trace();
- message+="\n+++ Internal PLUMED error";
+ message+="\n+++ PLUMED error";
if(file.length()>0) {
char cline[1000];
sprintf(cline,"%u",line);
@@ -61,34 +61,18 @@ std::string Exception::format(const std::string&msg,const std::string&file,unsig
}
-Exception::Exception():
- stackString(trace()),
- msg(format("","",0,""))
+Exception::Exception()
{
- abortIfExceptionsAreDisabled();
}
Exception::Exception(const std::string&msg):
- stackString(trace()),
msg(format(msg,"",0,""))
{
- abortIfExceptionsAreDisabled();
}
Exception::Exception(const std::string&msg,const std::string&file,unsigned line,const std::string&function):
- stackString(trace()),
msg(format(msg,file,line,function))
{
- abortIfExceptionsAreDisabled();
-}
-
-void Exception::abortIfExceptionsAreDisabled() {
-#if ! defined(__PLUMED_HAS_EXCEPTIONS)
- fprintf(stderr,"%s","Exceptions are disabled, aborting now\n");
- fprintf(stderr,"%s",what());
- fprintf(stderr,"\n");
- std::abort();
-#endif
}
}
diff --git a/src/tools/Exception.h b/src/tools/Exception.h
index 954ced590b7334983eee0e85cd68ad05bef2529d..2fa1d8d7372900341d1467c283c97cc5cbbeb882 100644
--- a/src/tools/Exception.h
+++ b/src/tools/Exception.h
@@ -66,11 +66,8 @@ check is only performed when NDEBUG macro is not defined. They should
be used when the check is expensive and should be skipped in production
code.
-By default, execution is terminated imediately and a message is printed on stderr.
-If PLUMED is compiled with -D__PLUMED_EXCEPTIONS execution will continue
-and the exception will be passed to c++, so that it will be possible
-to intercepted it at a higher level, even outside plumed.
+Exceptions can be caught within plumed or outside it.
E.g., in an external c++ code using PLUMED as a library, one can type
\verbatim
try{
@@ -96,15 +93,13 @@ is slower (GB)
class Exception : public std::exception
{
/// Stack trace at exception
- std::string stackString;
+ std::string stackString = trace();
/// Reported message
- std::string msg;
+ std::string msg = format("","",0,"");
/// Create stack trace
static std::string trace();
/// Common tool, invoked by all the constructor to build the message string
static std::string format(const std::string&,const std::string&,unsigned,const std::string&);
-/// Method which aborts in case exceptions are disabled
- void abortIfExceptionsAreDisabled();
public:
/// Without message
Exception();
diff --git a/src/tools/ForwardDecl.h b/src/tools/ForwardDecl.h
index 5e8fc253a18c43cd8ae48fc83a94c41e3a523280..461f4fe07a08f52275af8505df43a399dd2594ff 100644
--- a/src/tools/ForwardDecl.h
+++ b/src/tools/ForwardDecl.h
@@ -23,6 +23,7 @@
#define __PLUMED_tools_ForwardDecl_h
#include <memory>
+#include <utility>
namespace PLMD {
@@ -35,17 +36,20 @@ class ForwardDecl:
std::unique_ptr<T>
{
public:
-// Construction is only possible from a pointer.
- explicit ForwardDecl(T*);
+// Construction with arbitrary argument.
+ template<typename ...Args>
+ explicit ForwardDecl(Args &&...args);
// Dereference operator is inherited from std::unique_ptr<T>
using std::unique_ptr<T>::operator *;
};
template <class T>
-ForwardDecl<T>::ForwardDecl(T*x):
- std::unique_ptr<T>(x)
+template<typename ...Args>
+ForwardDecl<T>::ForwardDecl(Args &&...args):
+ std::unique_ptr<T>(new T(std::forward<Args>(args)...))
{}
+
}
#endif
diff --git a/src/tools/Grid.cpp b/src/tools/Grid.cpp
index 00fa5f3887ac5a8d1ca7380b59cc3559464361a1..51299bc0261e27ccd2e81a5867acbd9a0d2a7dfe 100644
--- a/src/tools/Grid.cpp
+++ b/src/tools/Grid.cpp
@@ -280,10 +280,10 @@ vector<Grid::index_t> Grid::getNeighbors
for(unsigned i=0; i<dimension_; ++i) {
int i0=small_indices[i]-nneigh[i]+indices[i];
if(!pbc_[i] && i0<0) continue;
- if(!pbc_[i] && i0>=nbin_[i]) continue;
+ if(!pbc_[i] && i0>=static_cast<int>(nbin_[i])) continue;
if( pbc_[i] && i0<0) i0=nbin_[i]-(-i0)%nbin_[i];
- if( pbc_[i] && i0>=nbin_[i]) i0%=nbin_[i];
- tmp_indices[ll]=((unsigned)i0);
+ if( pbc_[i] && i0>=static_cast<int>(nbin_[i])) i0%=nbin_[i];
+ tmp_indices[ll]=static_cast<unsigned>(i0);
ll++;
}
tmp_indices.resize(ll);
diff --git a/src/tools/IFile.cpp b/src/tools/IFile.cpp
index 7259eec5ad385846fffa8a5887cd7289b0610ae2..085c4ab925ca22d1e875c1e435c619698e7e0e28 100644
--- a/src/tools/IFile.cpp
+++ b/src/tools/IFile.cpp
@@ -48,7 +48,7 @@ size_t IFile::llread(char*ptr,size_t s) {
if(rr<0) err=true;
r=rr;
#else
- plumed_merror("trying to use a gz file without zlib being linked");
+ plumed_merror("file " + getPath() + ": trying to use a gz file without zlib being linked");
#endif
} else {
r=fread(ptr,1,s,fp);
@@ -94,7 +94,7 @@ IFile& IFile::advanceField() {
}
done=true;
} else if( !words.empty() ) {
- plumed_merror(getPath() + " mismatch between number of fields in file and expected number");
+ plumed_merror("file " + getPath() + ": mismatch between number of fields in file and expected number");
}
}
}
@@ -115,7 +115,7 @@ IFile& IFile::open(const std::string&path) {
#ifdef __PLUMED_HAS_ZLIB
gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"r");
#else
- plumed_merror("trying to use a gz file without zlib being linked");
+ plumed_merror("file " + getPath() + ": trying to use a gz file without zlib being linked");
#endif
}
if(plumed) plumed->insertFile(*this);
@@ -230,7 +230,9 @@ IFile& IFile::getline(std::string &str) {
unsigned IFile::findField(const std::string&name)const {
unsigned i;
for(i=0; i<fields.size(); i++) if(fields[i].name==name) break;
- if(i>=fields.size()) plumed_merror(name);
+ if(i>=fields.size()) {
+ plumed_merror("file " + getPath() + ": field " + name + " cannot be found");
+ }
return i;
}
diff --git a/src/tools/KernelFunctions.cpp b/src/tools/KernelFunctions.cpp
index f9f61cd375dcf36cb5463ac815df46ff7c420e2b..c514025709b25b40cdcf19677927b451c6da512c 100755
--- a/src/tools/KernelFunctions.cpp
+++ b/src/tools/KernelFunctions.cpp
@@ -65,7 +65,7 @@ The following variants are available.
</tr> <tr>
<td> gaussian </td> <td> \f$f(r) = \frac{1}{(2 \pi)^{n} \sqrt{|\Sigma^{-1}|}} \exp\left(-0.5 r^2 \right)\f$ </td>
</tr> <tr>
-<td> truncated-gaussian </td> <td> \f$f(r) = \frac{1}{(2 \pi)^{n} \sqrt{|\Sigma^{-1}|} \left(\frac{\erf(-6.25/sqrt{2}) - \erf(-6.25/sqrt{2})}{2}\right)^n} \exp\left(-0.5 r^2 \right)\f$ </td>
+<td> truncated-gaussian </td> <td> \f$f(r) = \frac{1}{(2 \pi)^{n} \sqrt{|\Sigma^{-1}|} \left(\frac{\mathrm{erf}(-6.25/sqrt{2}) - \mathrm{erf}(-6.25/sqrt{2})}{2}\right)^n} \exp\left(-0.5 r^2 \right)\f$ </td>
</tr> <tr>
<td> triangular </td> <td> \f$f(r) = \frac{3}{V} ( 1 - | r | )H(1-|r|) \f$ </td>
</tr> <tr>
@@ -160,9 +160,10 @@ void KernelFunctions::setData( const std::vector<double>& at, const std::vector<
void KernelFunctions::normalize( const std::vector<Value*>& myvals ) {
- double det; unsigned ncv=ndim();
+ double det=1.;
+ unsigned ncv=ndim();
if(dtype==diagonal) {
- det=1; for(unsigned i=0; i<width.size(); ++i) det*=width[i]*width[i];
+ for(unsigned i=0; i<width.size(); ++i) det*=width[i]*width[i];
} else if(dtype==multi) {
Matrix<double> mymatrix( getMatrix() ), myinv( ncv, ncv );
Invert(mymatrix,myinv); double logd;
@@ -273,8 +274,8 @@ std::vector<double> KernelFunctions::getContinuousSupport( ) const {
Invert(mymatrix,myinv);
Matrix<double> myautovec(ncv,ncv); std::vector<double> myautoval(ncv);
diagMat(myinv,myautoval,myautovec);
- double maxautoval; maxautoval=0.;
- unsigned ind_maxautoval;
+ double maxautoval=0.;
+ unsigned ind_maxautoval=0;
for (unsigned i=0; i<ncv; i++) {
if(myautoval[i]>maxautoval) {maxautoval=myautoval[i]; ind_maxautoval=i;}
}
@@ -340,7 +341,7 @@ double KernelFunctions::evaluate( const std::vector<Value*>& pos, std::vector<do
Matrix<double> mymatrix( getMatrix() );
for(unsigned i=0; i<mymatrix.nrows(); ++i) {
- double dp_i, dp_j; derivatives[i]=0;
+ derivatives[i]=0;
if( pos[i]->isPeriodic() ) {
r2+=2*( 1 - costmp[i] )*mymatrix(i,i);
} else {
@@ -382,12 +383,12 @@ double KernelFunctions::evaluate( const std::vector<Value*>& pos, std::vector<do
return kval;
}
-KernelFunctions* KernelFunctions::read( IFile* ifile, const bool& cholesky, const std::vector<std::string>& valnames ) {
+std::unique_ptr<KernelFunctions> KernelFunctions::read( IFile* ifile, const bool& cholesky, const std::vector<std::string>& valnames ) {
double h;
if( !ifile->scanField("height",h) ) return NULL;;
std::string sss; ifile->scanField("multivariate",sss);
- std::string ktype; ifile->scanField("kerneltype",ktype);
+ std::string ktype="gaussian"; if( ifile->FieldExist("kerneltype") ) ifile->scanField("kerneltype",ktype);
plumed_massert( sss=="false" || sss=="true" || sss=="von-misses", "multivariate flag must be either false, true or von-misses");
// Read the position of the center
@@ -401,7 +402,7 @@ KernelFunctions* KernelFunctions::read( IFile* ifile, const bool& cholesky, cons
ifile->scanField("sigma_"+valnames[i],sig[i]);
if( !cholesky ) sig[i]=sqrt(sig[i]);
}
- return new KernelFunctions( cc, sig, ktype, "DIAGONAL", h );
+ return std::unique_ptr<KernelFunctions>(new KernelFunctions( cc, sig, ktype, "DIAGONAL", h ) );
}
unsigned ncv=valnames.size();
@@ -419,8 +420,8 @@ KernelFunctions* KernelFunctions::read( IFile* ifile, const bool& cholesky, cons
for(unsigned i=0; i<ncv; i++) {
for(unsigned j=i; j<ncv; j++) { sig[k]=invmatrix(i,j); k++; }
}
- if( sss=="true" ) return new KernelFunctions( cc, sig, ktype, "MULTIVARIATE", h );
- return new KernelFunctions( cc, sig, ktype, "VON-MISSES", h );
+ if( sss=="true" ) return std::unique_ptr<KernelFunctions>(new KernelFunctions( cc, sig, ktype, "MULTIVARIATE", h ) );
+ return std::unique_ptr<KernelFunctions>(new KernelFunctions( cc, sig, ktype, "VON-MISSES", h ) );
}
}
diff --git a/src/tools/KernelFunctions.h b/src/tools/KernelFunctions.h
index 32966973eba45d7bdb1ce358a16705428a9dd8cd..ac26c23d33291bc8692ceff0cf9ec7d6be3241f0 100644
--- a/src/tools/KernelFunctions.h
+++ b/src/tools/KernelFunctions.h
@@ -26,6 +26,7 @@
#include "Matrix.h"
#include "core/Value.h"
#include <vector>
+#include <memory>
namespace PLMD {
@@ -64,7 +65,7 @@ public:
/// Evaluate the kernel function with constant intervals
double evaluate( const std::vector<Value*>& pos, std::vector<double>& derivatives, bool usederiv=true, bool doInt=false, double lowI_=-1, double uppI_=-1 ) const;
/// Read a kernel function from a file
- static KernelFunctions* read( IFile* ifile, const bool& cholesky, const std::vector<std::string>& valnames );
+ static std::unique_ptr<KernelFunctions> read( IFile* ifile, const bool& cholesky, const std::vector<std::string>& valnames );
};
inline
diff --git a/src/tools/MolDataClass.cpp b/src/tools/MolDataClass.cpp
index 3a90191f1115a1d80227ec8b3c5801512039c5ae..c7733871ae747bb7671c44408efa46e63070154e 100644
--- a/src/tools/MolDataClass.cpp
+++ b/src/tools/MolDataClass.cpp
@@ -58,6 +58,7 @@ bool MolDataClass::allowedResidue( const std::string& type, const std::string& r
// Terminal groups
else if(residuename=="ACE") return true;
else if(residuename=="NME") return true;
+ else if(residuename=="NH2") return true;
// Alternative residue names in common force fiels
else if(residuename=="GLH") return true; // neutral GLU
else if(residuename=="ASH") return true; // neutral ASP
@@ -141,7 +142,7 @@ void MolDataClass::getBackboneForResidue( const std::string& type, const unsigne
} else if( residuename=="ACE") {
atoms.resize(1);
atoms[0]=mypdb.getNamedAtomFromResidue("C",residuenum);
- } else if( residuename=="NME") {
+ } else if( residuename=="NME"||residuename=="NH2") {
atoms.resize(1);
atoms[0]=mypdb.getNamedAtomFromResidue("N",residuenum);
} else {
@@ -170,6 +171,7 @@ bool MolDataClass::isTerminalGroup( const std::string& type, const std::string&
if( type=="protein" ) {
if( residuename=="ACE" ) return true;
else if( residuename=="NME" ) return true;
+ else if( residuename=="NH2" ) return true;
else return false;
} else {
plumed_merror(type + " is not a valid molecule type");
diff --git a/src/tools/OFile.cpp b/src/tools/OFile.cpp
index 517f78c01e34e017206a4a85e887e13fc3b22e77..8c9fe837d4cce45a17728c450cff2fdd6470895f 100644
--- a/src/tools/OFile.cpp
+++ b/src/tools/OFile.cpp
@@ -52,7 +52,7 @@ size_t OFile::llwrite(const char*ptr,size_t s) {
#ifdef __PLUMED_HAS_ZLIB
r=gzwrite(gzFile(gzfp),ptr,s);
#else
- plumed_merror("trying to use a gz file without zlib being linked");
+ plumed_merror("file " + getPath() + ": trying to use a gz file without zlib being linked");
#endif
} else {
r=fwrite(ptr,1,s,fp);
@@ -83,7 +83,7 @@ OFile::OFile():
actual_buffer_length=0;
buffer.reset(new char [buflen]);
// these are set to zero to avoid valgrind errors
- for(unsigned i=0; i<buflen; ++i) buffer[i]=0;
+ for(int i=0; i<buflen; ++i) buffer[i]=0;
buffer_string.reset(new char [1000]);
// these are set to zero to avoid valgrind errors
for(unsigned i=0; i<1000; ++i) buffer_string[i]=0;
@@ -298,7 +298,7 @@ OFile& OFile::open(const std::string&path) {
#ifdef __PLUMED_HAS_ZLIB
gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"a9");
#else
- plumed_merror("trying to use a gz file without zlib being linked");
+ plumed_merror("file " + getPath() + ": trying to use a gz file without zlib being linked");
#endif
}
} else {
@@ -310,7 +310,7 @@ OFile& OFile::open(const std::string&path) {
#ifdef __PLUMED_HAS_ZLIB
gzfp=(void*)gzopen(const_cast<char*>(this->path.c_str()),"w9");
#else
- plumed_merror("trying to use a gz file without zlib being linked");
+ plumed_merror("file " + getPath() + ": trying to use a gz file without zlib being linked");
#endif
}
}
diff --git a/src/tools/OFile.h b/src/tools/OFile.h
index baa8732a1c8e7a2a2421c7838878705e4579f375..b330920ba6481500ceea07c46db183ecdc423053 100644
--- a/src/tools/OFile.h
+++ b/src/tools/OFile.h
@@ -157,7 +157,7 @@ class OFile:
/// Internal buffer length
int buflen;
/// This variables stores the actual buffer length
- unsigned actual_buffer_length;
+ int actual_buffer_length;
/// Class identifying a single field for fielded output
class Field:
public FieldBase {
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index ddbec1b2586dee7c0e31b3e1f412c71413072bb2..c719a9121b1ff35712261c9d16bb2854721d3f24 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -97,9 +97,9 @@ void RMSD::setReference(const vector<Vector> & reference) {
plumed_massert(displace.empty(),"you should first clear() an RMSD object, then set a new reference");
align.resize(n,1.0/n);
displace.resize(n,1.0/n);
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) reference_center+=this->reference[i]*align[i];
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) this->reference[i]-=reference_center;
reference_center_is_calculated=true;
reference_center_is_removed=true;
@@ -116,10 +116,10 @@ void RMSD::setAlign(const vector<double> & align, bool normalize_weights, bool r
this->align=align;
if(normalize_weights) {
double w=0.0;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) w+=this->align[i];
double inv=1.0/w;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) this->align[i]*=inv;
}
// recalculate the center anyway
@@ -149,11 +149,13 @@ void RMSD::setDisplace(const vector<double> & displace, bool normalize_weights)
plumed_massert(this->displace.size()==displace.size(),"mismatch in dimension of align/displace arrays");
this->displace=displace;
double w=0.0;
-#pragma ivdep
+ #pragma omp simd
for(unsigned i=0; i<n; i++) w+=this->displace[i];
double inv=1.0/w;
-#pragma ivdep
- if(normalize_weights) {for(unsigned i=0; i<n; i++) this->displace[i]*=inv;}
+ if(normalize_weights) {
+ #pragma omp simd
+ for(unsigned i=0; i<n; i++) this->displace[i]*=inv;
+ }
}
std::vector<double> RMSD::getDisplace() {
return displace;
@@ -971,7 +973,7 @@ void RMSDCoreData::doCoreCalc(bool safe,bool alEqDis, bool only_rotation) {
Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;
Vector cr; cr.zero(); if(!creference_is_removed)cr=creference;
// second expensive loop: compute second moments wrt centers
-#pragma ivdep
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
double w=align[iat];
rr00+=dotProduct(positions[iat]-cp,positions[iat]-cp)*w;
@@ -1082,15 +1084,16 @@ void RMSDCoreData::doCoreCalc(bool safe,bool alEqDis, bool only_rotation) {
// calculate rotation matrix derivatives and components distances needed for components only when align!=displacement
if(!alEqDis)ddist_drotation.zero();
-#pragma ivdep
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
// components differences: this is useful externally
d[iat]=positions[iat]-cp - matmul(rotation,reference[iat]-cr);
//cerr<<"D "<<iat<<" "<<d[iat][0]<<" "<<d[iat][1]<<" "<<d[iat][2]<<"\n";
-
- // ddist_drotation if needed
- if(!alEqDis or !only_rotation) ddist_drotation+=-2*displace[iat]*extProduct(d[iat],reference[iat]-cr);
}
+ // ddist_drotation if needed
+ if(!alEqDis or !only_rotation)
+ for (unsigned iat=0; iat<n; iat++)
+ ddist_drotation+=-2*displace[iat]*extProduct(d[iat],reference[iat]-cr);
if(!alEqDis or !only_rotation) {
ddist_drr01.zero();
@@ -1112,7 +1115,7 @@ double RMSDCoreData::getDistance( bool squared) {
dist=eigenvals[0]+rr00+rr11;
const unsigned n=static_cast<unsigned int>(reference.size());
double localDist = 0;
-#pragma simd reduction(+:localDist)
+ #pragma omp simd reduction(+:localDist)
for(unsigned iat=0; iat<n; iat++) {
if(alEqDis) {
if(safe) localDist+=align[iat]*modulo2(d[iat]);
@@ -1145,7 +1148,7 @@ void RMSDCoreData::doCoreCalcWithCloseStructure(bool safe,bool alEqDis, Tensor &
Tensor rotation = matmul(rotationPosClose, rotationRefClose);
-#pragma simd
+ #pragma omp simd
for (unsigned iat=0; iat<natoms; iat++) {
d[iat] = positions[iat] - cp - matmul(rotation, reference[iat]-cr);
}
@@ -1178,7 +1181,7 @@ std::vector<Vector> RMSDCoreData::getDDistanceDPositions() {
if(!isInitialized)plumed_merror("getDPositionsDerivatives needs to initialize the coreData first!");
Vector csum;
Vector tmp1,tmp2;
-#pragma ivdep
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
if(alEqDis) {
// there is no need for derivatives of rotation and shift here as it is by construction zero
@@ -1197,8 +1200,9 @@ std::vector<Vector> RMSDCoreData::getDDistanceDPositions() {
}
}
-#pragma ivdep
- if(!alEqDis) for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcpositions-csum)*align[iat]); }
+ if(!alEqDis)
+ #pragma omp simd
+ for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcpositions-csum)*align[iat]); }
return derivatives;
}
@@ -1220,7 +1224,7 @@ std::vector<Vector> RMSDCoreData::getDDistanceDReference() {
Tensor t_ddist_drr01=ddist_drr01.transpose();
// third expensive loop: derivatives
-#pragma simd
+ #pragma omp simd
for(unsigned iat=0; iat<n; iat++) {
if(alEqDis) {
// there is no need for derivatives of rotation and shift here as it is by construction zero
@@ -1240,8 +1244,9 @@ std::vector<Vector> RMSDCoreData::getDDistanceDReference() {
}
}
-#pragma ivdep
- if(!alEqDis) for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcreference-csum)*align[iat]);}
+ if(!alEqDis)
+ #pragma omp simd
+ for(unsigned iat=0; iat<n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcreference-csum)*align[iat]);}
return derivatives;
}
diff --git a/src/tools/SwitchingFunction.h b/src/tools/SwitchingFunction.h
index 907362caed68f1efb7c1e8cf38f5e14d2f4483f3..175659813dc41d9616997a0bfc3d6122436da566 100644
--- a/src/tools/SwitchingFunction.h
+++ b/src/tools/SwitchingFunction.h
@@ -56,7 +56,7 @@ class SwitchingFunction {
int mm=0;
/// Parameters for smap function
int a=0;
- int b=b;
+ int b=0;
double c=0.0;
double d=0.0;
// nativeq
diff --git a/src/tools/Tools.cpp b/src/tools/Tools.cpp
index 1813c02c2897e408f2bdfb750f58aab888472ff5..25b9bd91b9c1018a106459b54347a6efa4724dc5 100644
--- a/src/tools/Tools.cpp
+++ b/src/tools/Tools.cpp
@@ -189,7 +189,7 @@ bool Tools::getParsedLine(IFile& ifile,vector<string> & words) {
if(!w.empty()) {
if(inside && *(w.begin())=="...") {
inside=false;
- if(w.size()==2) plumed_massert(w[1]==words[0],"second word in terminating \"...\" lines, if present, should be equal to first word of directive");
+ if(w.size()==2) plumed_massert(w[1]==words[0],"second word in terminating \"...\" "+w[1]+" line, if present, should be equal to first word of directive: "+words[0]);
plumed_massert(w.size()<=2,"terminating \"...\" lines cannot consist of more than two words");
w.clear();
} else if(*(w.end()-1)=="...") {
@@ -252,7 +252,7 @@ bool Tools::getKey(vector<string>& line,const string & key,string & s,int rep) {
if(rep>=0 && startWith(s,multi)) {
s=s.substr(multi.length(),s.length());
std::vector<std::string> words=getWords(s,"\t\n ,");
- plumed_massert(rep<words.size(),"Number of fields in " + s + " not consistent with number of replicas");
+ plumed_massert(rep<static_cast<int>(words.size()),"Number of fields in " + s + " not consistent with number of replicas");
s=words[rep];
}
return true;
diff --git a/src/tools/Tools.h b/src/tools/Tools.h
index 4b15ec2dfe92fdfd81bc35f7dbea4b31547a4cad..1b3b70e55340970a2fcecbc385ab4fbb97fc23f7 100644
--- a/src/tools/Tools.h
+++ b/src/tools/Tools.h
@@ -151,7 +151,6 @@ template <class T>
bool Tools::parseVector(std::vector<std::string>&line,const std::string&key,std::vector<T>&val,int rep) {
std::string s;
if(!getKey(line,key+"=",s,rep)) return false;
-// if(s.length()==0) return true;
val.clear();
std::vector<std::string> words=getWords(s,"\t\n ,");
for(unsigned i=0; i<words.size(); ++i) {
@@ -161,7 +160,7 @@ bool Tools::parseVector(std::vector<std::string>&line,const std::string&key,std:
if(rep>=0 && startWith(s,multi)) {
s=s.substr(multi.length(),s.length());
std::vector<std::string> words=getWords(s,"\t\n ,");
- plumed_assert(rep<words.size());
+ plumed_assert(rep<static_cast<int>(words.size()));
s=words[rep];
}
if(!convert(s,v))return false;
diff --git a/src/vatom/COM.cpp b/src/vatom/COM.cpp
index 9e9ac4890c41a0b3ca94619586f085f5a394a8a7..da0259c9095b255400da1f2e9cf3779c72120086 100644
--- a/src/vatom/COM.cpp
+++ b/src/vatom/COM.cpp
@@ -98,7 +98,7 @@ COM::COM(const ActionOptions&ao):
log.printf(" %d",atoms[i].serial());
}
log.printf("\n");
- if(!nopbc) {
+ if(nopbc) {
log<<" PBC will be ignored\n";
} else {
log<<" broken molecules will be rebuilt assuming atoms are in the proper order\n";
diff --git a/src/vatom/Center.cpp b/src/vatom/Center.cpp
index 70269b52c732ca346c5914a73314dc92c73d3f88..29d59349430e9cffeb6725b96de15f85e5321c89 100644
--- a/src/vatom/Center.cpp
+++ b/src/vatom/Center.cpp
@@ -131,7 +131,7 @@ Center::Center(const ActionOptions&ao):
log.printf("\n");
}
}
- if(!nopbc) {
+ if(nopbc) {
log<<" PBC will be ignored\n";
} else {
log<<" broken molecules will be rebuilt assuming atoms are in the proper order\n";
diff --git a/src/ves/BF_Cosine.cpp b/src/ves/BF_Cosine.cpp
index 5428cbcf2b07a1a80bd3219da8d86cd37f9dd8e1..50f18cd322defaff78c470bcb3f9b46be81a8e5b 100644
--- a/src/ves/BF_Cosine.cpp
+++ b/src/ves/BF_Cosine.cpp
@@ -54,6 +54,15 @@ f_{n}(x) &= cos(n \cdot \frac{2\pi}{P} x) \\
f_{N}(x) &= cos(N \cdot \frac{2\pi}{P} x) \\
\f}
where \f$P=(b-a)\f$ is the periodicity of the interval.
+They are orthogonal over the interval \f$[a,b]\f$
+\f[
+\int_{a}^{b} dx \, f_{n}(x)\, f_{m}(x) =
+\begin{cases}
+0 & n \neq m \\
+(b-a) & n = m = 0 \\
+(b-a)/2 & n = m \neq 0
+\end{cases}.
+\f]
\par Examples
diff --git a/src/ves/BF_Fourier.cpp b/src/ves/BF_Fourier.cpp
index 3e1dd3cbf20d2dc77a7b72cee22c43b6617902d7..7cc62a52cd9f5d4c4292b089280ca287bbab6e9a 100644
--- a/src/ves/BF_Fourier.cpp
+++ b/src/ves/BF_Fourier.cpp
@@ -49,13 +49,23 @@ f_{2}(x) &= sin(\frac{2\pi }{P} x) \\
f_{3}(x) &= cos(2 \cdot \frac{2\pi}{P} x) \\
f_{4}(x) &= sin(2 \cdot \frac{2\pi}{P} x) \\
& \vdots \\
-f_{2n-1}(x) &= cos(n \cdot \frac{2\pi}{P} x) \\
-f_{2n}(x) &= sin(n \cdot \frac{2\pi}{P} x) \\
+f_{2k-1}(x) &= cos(k \cdot \frac{2\pi}{P} x) \\
+f_{2k}(x) &= sin(k \cdot \frac{2\pi}{P} x) \\
& \vdots \\
f_{2N-1}(x) &= cos(N \cdot \frac{2\pi}{P} x) \\
f_{2N}(x) &= sin(N \cdot \frac{2\pi}{P} x) \\
\f}
where \f$P=(b-a)\f$ is the periodicity of the interval.
+They are orthogonal over the interval \f$[a,b]\f$
+\f[
+\int_{a}^{b} dx \, f_{n}(x)\, f_{m}(x) =
+\begin{cases}
+0 & n \neq m \\
+(b-a) & n = m = 0 \\
+(b-a)/2 & n = m \neq 0
+\end{cases}.
+\f]
+
\par Examples
diff --git a/src/ves/BF_Sine.cpp b/src/ves/BF_Sine.cpp
index 6ff1ac2c625365a1238df82ba109a823479b5512..6203b8727b749b53ce1f5a4d8d1b8216a6701b93 100644
--- a/src/ves/BF_Sine.cpp
+++ b/src/ves/BF_Sine.cpp
@@ -54,6 +54,15 @@ f_{n}(x) &= sin(n \cdot \frac{2\pi}{P} x) \\
f_{N}(x) &= sin(N \cdot \frac{2\pi}{P} x) \\
\f}
where \f$P=(b-a)\f$ is the periodicity of the interval.
+They are orthogonal over the interval \f$[a,b]\f$
+\f[
+\int_{a}^{b} dx \, f_{n}(x)\, f_{m}(x) =
+\begin{cases}
+0 & n \neq m \\
+(b-a) & n = m = 0 \\
+(b-a)/2 & n = m \neq 0
+\end{cases}.
+\f]
\par Examples
diff --git a/src/ves/LinearBasisSetExpansion.cpp b/src/ves/LinearBasisSetExpansion.cpp
index e17e14852fede47c3743ecc4d1e40841c4526c3f..f4f5cf422d15659635c634b74ab39bc7a3a1f59e 100644
--- a/src/ves/LinearBasisSetExpansion.cpp
+++ b/src/ves/LinearBasisSetExpansion.cpp
@@ -422,6 +422,7 @@ double LinearBasisSetExpansion::getBiasAndForces(const std::vector<double>& args
}
//
if(comm_in!=NULL) {
+ // coeffsderivs_values is not summed as the mpi Sum is done later on for the averages
comm_in->Sum(bias);
comm_in->Sum(forces);
}
@@ -468,6 +469,31 @@ void LinearBasisSetExpansion::getBasisSetValues(const std::vector<double>& args_
}
+double LinearBasisSetExpansion::getBasisSetValue(const std::vector<double>& args_values, const size_t index, std::vector<BasisFunctions*>& basisf_pntrs_in, CoeffsVector* coeffs_pntr_in) {
+ unsigned int nargs = args_values.size();
+ plumed_assert(coeffs_pntr_in->numberOfDimensions()==nargs);
+ plumed_assert(basisf_pntrs_in.size()==nargs);
+
+ std::vector<double> args_values_trsfrm(nargs);
+ std::vector< std::vector <double> > bf_values;
+ //
+ for(unsigned int k=0; k<nargs; k++) {
+ std::vector<double> tmp_val(basisf_pntrs_in[k]->getNumberOfBasisFunctions());
+ std::vector<double> tmp_der(tmp_val.size());
+ bool inside=true;
+ basisf_pntrs_in[k]->getAllValues(args_values[k],args_values_trsfrm[k],inside,tmp_val,tmp_der);
+ bf_values.push_back(tmp_val);
+ }
+ //
+ std::vector<unsigned int> indices=coeffs_pntr_in->getIndices(index);
+ double bf_value=1.0;
+ for(unsigned int k=0; k<nargs; k++) {
+ bf_value*=bf_values[k][indices[k]];
+ }
+ return bf_value;
+}
+
+
void LinearBasisSetExpansion::setupUniformTargetDistribution() {
std::vector< std::vector <double> > bf_integrals(0);
std::vector<double> targetdist_averages(ncoeffs_,0.0);
@@ -551,6 +577,7 @@ void LinearBasisSetExpansion::calculateTargetDistAveragesFromGrid(const Grid* ta
for(Grid::index_t l=rank; l<targetdist_grid_pntr->getSize(); l+=stride) {
std::vector<double> args_values = targetdist_grid_pntr->getPoint(l);
std::vector<double> basisset_values(ncoeffs_);
+ // parallelization done over the grid -> should NOT use parallel in getBasisSetValues!!
getBasisSetValues(args_values,basisset_values,false);
double weight = integration_weights[l]*targetdist_grid_pntr->getValue(l);
for(unsigned int i=0; i<ncoeffs_; i++) {
@@ -559,7 +586,7 @@ void LinearBasisSetExpansion::calculateTargetDistAveragesFromGrid(const Grid* ta
}
mycomm_.Sum(targetdist_averages);
// the overall constant;
- targetdist_averages[0] = 1.0;
+ targetdist_averages[0] = getBasisSetConstant();
TargetDistAverages() = targetdist_averages;
}
diff --git a/src/ves/LinearBasisSetExpansion.h b/src/ves/LinearBasisSetExpansion.h
index a7872d216c371f3fae82fafe0a54dc0c71cf959c..e4e581b1a60b46da4b51ea3e64a3f1ab87466bf1 100644
--- a/src/ves/LinearBasisSetExpansion.h
+++ b/src/ves/LinearBasisSetExpansion.h
@@ -125,6 +125,10 @@ public:
//
static void getBasisSetValues(const std::vector<double>&, std::vector<double>&, std::vector<BasisFunctions*>&, CoeffsVector*, Communicator* comm_in=NULL);
void getBasisSetValues(const std::vector<double>&, std::vector<double>&, const bool parallel=true);
+ //
+ static double getBasisSetValue(const std::vector<double>&, const size_t, std::vector<BasisFunctions*>&, CoeffsVector*);
+ double getBasisSetValue(const std::vector<double>&, const size_t);
+ double getBasisSetConstant();
// Bias grid and output stuff
void setupBiasGrid(const bool usederiv=false);
void updateBiasGrid();
@@ -224,6 +228,19 @@ void LinearBasisSetExpansion::getBasisSetValues(const std::vector<double>& args_
}
+inline
+double LinearBasisSetExpansion::getBasisSetValue(const std::vector<double>& args_values, const size_t basisset_index) {
+ return getBasisSetValue(args_values,basisset_index,basisf_pntrs_, bias_coeffs_pntr_);
+}
+
+
+inline
+double LinearBasisSetExpansion::getBasisSetConstant() {
+ std::vector<double> args_dummy(nargs_,0.0);
+ return getBasisSetValue(args_dummy,0,basisf_pntrs_, bias_coeffs_pntr_);
+}
+
+
}
}
diff --git a/src/ves/Opt_BachAveragedSGD.cpp b/src/ves/Opt_BachAveragedSGD.cpp
index eeaffda49780fdf2609d7182265c98b23dd98465..28a4ae5de277668b9b8b08043660971c4047ad4f 100644
--- a/src/ves/Opt_BachAveragedSGD.cpp
+++ b/src/ves/Opt_BachAveragedSGD.cpp
@@ -206,7 +206,7 @@ void Opt_BachAveragedSGD::registerKeywords(Keywords& keys) {
Optimizer::useHessianKeywords(keys);
Optimizer::useMaskKeywords(keys);
Optimizer::useRestartKeywords(keys);
- // Optimizer::useMonitorAveragesKeywords(keys);
+ Optimizer::useMonitorAverageGradientKeywords(keys);
Optimizer::useDynamicTargetDistributionKeywords(keys);
keys.add("hidden","COMBINED_GRADIENT_FILE","the name of output file for the combined gradient (gradient + Hessian term)");
keys.add("hidden","COMBINED_GRADIENT_OUTPUT","how often the combined gradient should be written to file. This parameter is given as the number of bias iterations. It is by default 100 if COMBINED_GRADIENT_FILE is specficed");
diff --git a/src/ves/Opt_Dummy.cpp b/src/ves/Opt_Dummy.cpp
index 35bd5ce261921209e2d9ce4a9213abab3a5a7f35..795b4502d874a668b2b05a191b26e88f5a4f9e3e 100644
--- a/src/ves/Opt_Dummy.cpp
+++ b/src/ves/Opt_Dummy.cpp
@@ -90,6 +90,7 @@ void Opt_Dummy::registerKeywords(Keywords& keys) {
//
Optimizer::useMultipleWalkersKeywords(keys);
Optimizer::useHessianKeywords(keys);
+ Optimizer::useMonitorAverageGradientKeywords(keys);
keys.addFlag("MONITOR_HESSIAN",false,"also monitor the Hessian");
}
diff --git a/src/ves/Optimizer.cpp b/src/ves/Optimizer.cpp
index b7785f3661583eb4227a37d8de19088c2e0a5a75..74f28aea5473f8c61b6ff2ed3d6725306dc8644b 100644
--- a/src/ves/Optimizer.cpp
+++ b/src/ves/Optimizer.cpp
@@ -48,6 +48,7 @@ Optimizer::Optimizer(const ActionOptions&ao):
iter_counter(0),
use_hessian_(false),
diagonal_hessian_(true),
+ monitor_instantaneous_gradient_(false),
use_mwalkers_mpi_(false),
mwalkers_mpi_single_files_(true),
dynamic_targetdists_(0),
@@ -275,12 +276,16 @@ Optimizer::Optimizer(const ActionOptions&ao):
}
}
+ if(keywords.exists("MONITOR_INSTANTANEOUS_GRADIENT")) {
+ parseFlag("MONITOR_INSTANTANEOUS_GRADIENT",monitor_instantaneous_gradient_);
+ }
+
if(keywords.exists("MONITOR_AVERAGE_GRADIENT")) {
bool monitor_aver_gradient = false;
parseFlag("MONITOR_AVERAGE_GRADIENT",monitor_aver_gradient);
if(monitor_aver_gradient) {
unsigned int averaging_exp_decay=0;
- parse("MONITOR_AVERAGES_EXP_DECAY",averaging_exp_decay);
+ parse("MONITOR_AVERAGES_GRADIENT_EXP_DECAY",averaging_exp_decay);
aver_gradient_pntrs_.clear();
for(unsigned int i=0; i<ncoeffssets_; i++) {
CoeffsVector* aver_gradient_tmp = new CoeffsVector(*gradient_pntrs_[i]);
@@ -709,9 +714,11 @@ Optimizer::Optimizer(const ActionOptions&ao):
if(ncoeffssets_==1) {
log.printf(" Output Components:\n");
log.printf(" ");
- addComponent("gradrms"); componentIsNotPeriodic("gradrms");
- log.printf(" ");
- addComponent("gradmax"); componentIsNotPeriodic("gradmax");
+ if(monitor_instantaneous_gradient_) {
+ addComponent("gradrms"); componentIsNotPeriodic("gradrms");
+ log.printf(" ");
+ addComponent("gradmax"); componentIsNotPeriodic("gradmax");
+ }
if(aver_gradient_pntrs_.size()>0) {
log.printf(" ");
addComponent("avergradrms"); componentIsNotPeriodic("avergradrms");
@@ -729,9 +736,11 @@ Optimizer::Optimizer(const ActionOptions&ao):
log.printf(" Output Components for coefficent set %u:\n",i);
std::string is=""; Tools::convert(i,is); is = "_" + coeffssetid_prefix_ + is;
log.printf(" ");
- addComponent("gradrms"+is); componentIsNotPeriodic("gradrms"+is);
- log.printf(" ");
- addComponent("gradmax"+is); componentIsNotPeriodic("gradmax"+is);
+ if(monitor_instantaneous_gradient_) {
+ addComponent("gradrms"+is); componentIsNotPeriodic("gradrms"+is);
+ log.printf(" ");
+ addComponent("gradmax"+is); componentIsNotPeriodic("gradmax"+is);
+ }
if(aver_gradient_pntrs_.size()>0) {
log.printf(" ");
addComponent("avergradrms"+is); componentIsNotPeriodic("avergradrms"+is);
@@ -837,8 +846,10 @@ void Optimizer::registerKeywords( Keywords& keys ) {
//
keys.reserveFlag("START_OPTIMIZATION_AFRESH",false,"if the iterations should be started afresh when a restart has been triggered by the RESTART keyword or the MD code.");
//
- keys.reserveFlag("MONITOR_AVERAGE_GRADIENT",false,"if the averaged gradient should be monitored.");
- keys.reserve("optional","MONITOR_AVERAGES_EXP_DECAY","use an exponentially decaying averaging with a given time constant when monitoring the averaged gradient");
+ keys.addFlag("MONITOR_INSTANTANEOUS_GRADIENT",false,"if quantities related to the instantaneous gradient should be outputted.");
+ //
+ keys.reserveFlag("MONITOR_AVERAGE_GRADIENT",false,"if the averaged gradient should be monitored and quantities related to it should be outputted.");
+ keys.reserve("optional","MONITOR_AVERAGES_GRADIENT_EXP_DECAY","use an exponentially decaying averaging with a given time constant when monitoring the averaged gradient");
//
keys.reserve("optional","TARGETDIST_STRIDE","stride for updating a target distribution that is iteratively updated during the optimization. Note that the value is given in terms of coefficent iterations.");
keys.reserve("optional","TARGETDIST_OUTPUT","how often the dynamic target distribution(s) should be written out to file. Note that the value is given in terms of coefficent iterations.");
@@ -859,8 +870,8 @@ void Optimizer::registerKeywords( Keywords& keys ) {
keys.use("UPDATE_FROM");
keys.use("UPDATE_UNTIL");
// Components that are always active
- keys.addOutputComponent("gradrms","default","the root mean square value of the coefficent gradient. For multiple biases this component is labeled using the number of the bias as gradrms-#.");
- keys.addOutputComponent("gradmax","default","the largest absolute value of the coefficent gradient. For multiple biases this component is labeled using the number of the bias as gradmax-#.");
+ keys.addOutputComponent("gradrms","MONITOR_INSTANTANEOUS_GRADIENT","the root mean square value of the coefficent gradient. For multiple biases this component is labeled using the number of the bias as gradrms-#.");
+ keys.addOutputComponent("gradmax","MONITOR_INSTANTANEOUS_GRADIENT","the largest absolute value of the coefficent gradient. For multiple biases this component is labeled using the number of the bias as gradmax-#.");
ActionWithValue::useCustomisableComponents(keys);
// keys.addOutputComponent("gradmaxidx","default","the index of the maximum absolute value of the gradient");
@@ -902,9 +913,11 @@ void Optimizer::useRestartKeywords(Keywords& keys) {
}
-void Optimizer::useMonitorAveragesKeywords(Keywords& keys) {
+void Optimizer::useMonitorAverageGradientKeywords(Keywords& keys) {
keys.use("MONITOR_AVERAGE_GRADIENT");
- keys.use("MONITOR_AVERAGES_EXP_DECAY");
+ keys.use("MONITOR_AVERAGES_GRADIENT_EXP_DECAY");
+ keys.addOutputComponent("avergradrms","MONITOR_AVERAGE_GRADIENT","the root mean square value of the averaged coefficent gradient. For multiple biases this component is labeled using the number of the bias as gradrms-#.");
+ keys.addOutputComponent("avergradmax","MONITOR_AVERAGE_GRADIENT","the largest absolute value of the averaged coefficent gradient. For multiple biases this component is labeled using the number of the bias as gradmax-#.");
}
@@ -1074,12 +1087,15 @@ void Optimizer::updateOutputComponents() {
if(!fixed_stepsize_) {
getPntrToComponent("stepsize")->set( getCurrentStepSize(0) );
}
- getPntrToComponent("gradrms")->set( gradient_pntrs_[0]->getRMS() );
- size_t gradient_maxabs_idx=0;
- getPntrToComponent("gradmax")->set( gradient_pntrs_[0]->getMaxAbsValue(gradient_maxabs_idx) );
+ if(monitor_instantaneous_gradient_) {
+ getPntrToComponent("gradrms")->set( gradient_pntrs_[0]->getRMS() );
+ size_t gradient_maxabs_idx=0;
+ getPntrToComponent("gradmax")->set( gradient_pntrs_[0]->getMaxAbsValue(gradient_maxabs_idx) );
+ }
if(aver_gradient_pntrs_.size()>0) {
getPntrToComponent("avergradrms")->set( aver_gradient_pntrs_[0]->getRMS() );
- getPntrToComponent("avergradmax")->set( aver_gradient_pntrs_[0]->getMaxAbsValue(gradient_maxabs_idx) );
+ size_t avergradient_maxabs_idx=0;
+ getPntrToComponent("avergradmax")->set( aver_gradient_pntrs_[0]->getMaxAbsValue(avergradient_maxabs_idx) );
}
}
else {
@@ -1088,12 +1104,15 @@ void Optimizer::updateOutputComponents() {
if(!fixed_stepsize_) {
getPntrToComponent("stepsize"+is)->set( getCurrentStepSize(i) );
}
- getPntrToComponent("gradrms"+is)->set( gradient_pntrs_[i]->getRMS() );
- size_t gradient_maxabs_idx=0;
- getPntrToComponent("gradmax"+is)->set( gradient_pntrs_[i]->getMaxAbsValue(gradient_maxabs_idx) );
+ if(monitor_instantaneous_gradient_) {
+ getPntrToComponent("gradrms"+is)->set( gradient_pntrs_[i]->getRMS() );
+ size_t gradient_maxabs_idx=0;
+ getPntrToComponent("gradmax"+is)->set( gradient_pntrs_[i]->getMaxAbsValue(gradient_maxabs_idx) );
+ }
if(aver_gradient_pntrs_.size()>0) {
getPntrToComponent("avergradrms"+is)->set( aver_gradient_pntrs_[0]->getRMS() );
- getPntrToComponent("avergradmax"+is)->set( aver_gradient_pntrs_[0]->getMaxAbsValue(gradient_maxabs_idx) );
+ size_t avergradient_maxabs_idx=0;
+ getPntrToComponent("avergradmax"+is)->set( aver_gradient_pntrs_[0]->getMaxAbsValue(avergradient_maxabs_idx) );
}
}
}
diff --git a/src/ves/Optimizer.h b/src/ves/Optimizer.h
index 6e49dc2b1ed6d45d1ed2bba2d71d9a4492cf7f3d..c0209c214e47bd2d51071519396e921b7b3bbd11 100644
--- a/src/ves/Optimizer.h
+++ b/src/ves/Optimizer.h
@@ -67,6 +67,8 @@ private:
bool diagonal_hessian_;
bool hessian_covariance_from_averages_;
//
+ bool monitor_instantaneous_gradient_;
+ //
bool use_mwalkers_mpi_;
bool mwalkers_mpi_single_files_;
//
@@ -161,7 +163,7 @@ public:
static void useDynamicStepSizeKeywords(Keywords&);
static void useMaskKeywords(Keywords&);
static void useRestartKeywords(Keywords&);
- static void useMonitorAveragesKeywords(Keywords&);
+ static void useMonitorAverageGradientKeywords(Keywords&);
static void useDynamicTargetDistributionKeywords(Keywords&);
static void useReweightFactorKeywords(Keywords&);
//
diff --git a/src/ves/VesBias.cpp b/src/ves/VesBias.cpp
index 10a5b95523bcb317cb995d96b43fa79d3c2c0423..19fa945ea475e67a8ac221ee2666493aa468deb9 100644
--- a/src/ves/VesBias.cpp
+++ b/src/ves/VesBias.cpp
@@ -755,7 +755,7 @@ void VesBias::updateReweightFactor() {
double value = calculateReweightFactor();
getPntrToComponent("rct")->set(value);
}
-};
+}
double VesBias::calculateReweightFactor() const {
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index 31f1644a5a55fa839af0e1f426bbb419157beaae..aa7fec62872de8369ffa5348058cd8468804aa88 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -56,7 +56,6 @@ ActionWithVessel::ActionWithVessel(const ActionOptions&ao):
noderiv(true),
actionIsBridged(false),
nactive_tasks(0),
- stopwatch_fwd(new Stopwatch),
dertime_can_be_off(false),
dertime(true),
contributorsAreUnlocked(false),
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index 8cddbf9f71f8e565165a7206ea0cb8c9133c056d..b14c707d92afaffdc06139d9f991c305f20b835f 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -235,7 +235,7 @@ ALIASES = \
"issue{1}=<a href=\"http://github.com/plumed/plumed2/issues/\1\">#\1</a>" \
"branch{1}=<a href=\"http://github.com/plumed/plumed2/commits/\1\">\1</a>" \
"highlight{1}=\htmlonly<span style=\"background-color:yellow\">\endhtmlonly\1\htmlonly</span>\endhtmlonly" \
- "tarball{1}=<a href=\"tutorial-resources/\1.tar.gz\" style=\"font-weight:bold\" style=\"color:green\" download=\"\1.tar.gz\"> TARBALL </a>" \
+ "tarball{1}=\htmlonly<span style=\"background-color:yellow\">\endhtmlonly<a href=\"tutorial-resources/\1.tar.gz\" style=\"font-weight:bold\" style=\"color:green\" download=\"\1.tar.gz\"> TARBALL </a>\htmlonly</span>\endhtmlonly" \
"plumedfile=\verbatim BEGIN_PLUMED_FILE" \
"endplumedfile=\endverbatim" \
"plumednotmaintained=\warning This branch is not maintained. Users are invited to upgrade to a newer version"
diff --git a/user-doc/Installation.md b/user-doc/Installation.md
index 82ea3ebf684bc77e686b1301f1352a3e260233b2..e9fcfbe4620049851af5d1107cddd596410d2fbe 100644
--- a/user-doc/Installation.md
+++ b/user-doc/Installation.md
@@ -174,17 +174,32 @@ This might be useful when installing PLUMED within package managers such as MacP
make sure that only desired libraries are linked and thus to avoid to introduce spurious
dependencies. The only exception to this rule is `-ldl`, which is anyway a system library on Linux.
-\warning On Linux you might have problems using the LDFLAGS option. In particular,
-if makefile complaints that it cannot link the file 'src/lib/plumed-shared',
-try to set correctly
-the runtime path by using
-\verbatim
-> ./configure LDFLAGS="-L/opt/local/lib -Wl,-rpath,/opt/local/lib" \
- CPPFLAGS=-I/opt/local/include LIBS=-lmyxdrfile
-\endverbatim
-Notice that although the file 'src/lib/plumed-shared' is not necessary, being
+\warning On OSX it is common practice to hardcode the full path
+to libraries in the libraries themselves. This means that, after having linked
+a shared library, that specific shared library will be searched in the same
+place (we do the same for the `libplumed.dylib` library, which has an install name hardcoded).
+On the other hand, on Linux it is common pratice not to hardcode the full path.
+This means that if you use the `LDFLAGS` option to specify the path
+to the libraries you want to link to PLUMED (e.g. `./configure LDFLAGS="-L/path"`)
+these libraries might not be found later.
+The visible symptom is that `src/lib/plumed-shared` will not be linked correctly.
+Although the file 'src/lib/plumed-shared' is not necessary, being
able to produce it means that it will be possible to link PLUMED dynamically
with MD codes later.
+The easiest solution is to hardcode the library search path in this way:
+\verbatim
+> ./configure LDFLAGS="-L/path -Wl,-rpath,/path"
+\endverbatim
+Notice that as of PLUMED v2.4 it is possible to use the configure option `--enable-rpath`
+to automatically hardcode the path defined in `LIBRARY_PATH`:
+\verbatim
+> ./configure LIBRARY_PATH=/path --enable-rpath
+\endverbatim
+In this way, the search path used at link time (`LIBRARY_PATH`) and the one saved in the `libplumed.so`
+library will be consistent by construction.
+In a typical environment configured using module framework (http://modules.sourceforge.net),
+`LIBRARY_PATH` will be a variable containing the path to all the modules loaded at compilation
+time.
PLUMED needs blas and lapack. These are treated slighty different from
other libraries. The search is done in the usual way (i.e., first
@@ -273,14 +288,23 @@ you need to download the SOURCE of VMD, which contains
a plugins directory. Adapt build.sh and compile it. At
the end, you should get the molfile plugins compiled as a static
library `libmolfile_plugin.a`. Locate said file and `libmolfile_plugin.h`,
-and customize the configure command with something along
-the lines of:
+they should be in a directory called `/pathtovmdplugins/ARCH/molfile`
+(e.g. `/pathtovmdplugins/MACOSXX86_64/molfile`). Also locate file `molfile_plugin.h`,
+which should be in `/pathtovmdplugins/include`.
+Then customize the configure command with something along the lines of:
\verbatim
-./configure LDFLAGS="-ltcl8.5 -L/mypathtomolfilelibrary/ -L/mypathtotcl" CPPFLAGS="-I/mypathtolibmolfile_plugin.h/"
+./configure LDFLAGS="-L/pathtovmdplugins/ARCH/molfile" CPPFLAGS="-I/pathtovmdplugins/include -I/pathtovmdplugins/ARCH/molfile"
\endverbatim
-and rebuild.
+Notice that it might be necessary to add to `LDFLAGS` the path to your TCL interpreter, e.g.
+
+\verbatim
+./configure LDFLAGS="-ltcl8.5 -L/mypathtotcl -L/pathtovmdplugins/ARCH/molfile" \
+ CPPFLAGS="-I/pathtovmdplugins/include -I/pathtovmdplugins/ARCH/molfile"
+\endverbatim
+
+Then, rebuild plumed.
\section CompilingPlumed Compiling PLUMED
@@ -528,14 +552,18 @@ Notice that plumed comes with many variants that can be inspected with the comma
> sudo port info plumed
Plumed uses variants to support different compilers.
-For instance, you can install plumed with openmpi using
+For instance, you can install plumed with mpich using
- > sudo port install plumed +openmpi
+ > sudo port install plumed +mpich
-Using gcc instead of native compilers is recommended so as to
+Using more recent clang instead of native compilers is recommended so as to
take advantage of openMP
- > sudo port install plumed +openmpi +gcc7
+ > sudo port install plumed +mpich +clang50
+
+Notice that support for c++11 with gcc compilers is someway problematic within MacPorts
+due to impossibility to use the system c++ library. For this reason, only clang compilers are supported
+(see also [this discussion](https://github.com/macports/macports-ports/pull/1252)).
Variants can be also used to compile with debug flags (`+debug`), to pick a linear algebra library
(e.g. `+openblas`) and to enable all optional modules (`+allmodules`).
@@ -552,18 +580,18 @@ under the subport `plumed-devel` that can be installed with
It is also possible to install a plumed-patched version of gromacs.
For instance, you can use the following command to install
-gromacs patched with plumed with gcc compiler and openmpi:
+gromacs patched with plumed with clang-5.0 compiler and mpich:
- > sudo port install plumed +openmpi +gcc7
- > sudo port install gromacs-plumed +openmpi +gcc7
+ > sudo port install plumed +mpich +clang50
+ > sudo port install gromacs-plumed +mpich +clang50
In case you want to combine gromacs with the unstable version of plumed, use this instead:
- > sudo port install plumed-devel +openmpi +gcc7
- > sudo port install gromacs-plumed +openmpi +gcc7
+ > sudo port install plumed-devel +mpich +clang50
+ > sudo port install gromacs-plumed +mpich +clang50
Notice that gromacs should be compiled using the same compiler
-variant as plumed (in this example `+openmpi +gcc7`). In case this is not
+variant as plumed (in this example `+mpich +clang50`). In case this is not
true, compilation will fail.
Also notice that gromacs is patched with plumed in runtime mode
@@ -625,7 +653,7 @@ PLUMED version with different optimization levels.
Using modules, it is not necessary to make the PLUMED module explicitly dependent on the used library. Imagine a
scenario where you first installed a module `libxdrfile`, then load it while you compile PLUMED. If you
-provide the following option to configure `LDFLAGS="-Wl,-rpath,$LD_LIBRARY_PATH"`, the PLUMED executable and
+provide the following option to configure `--enable-rpath`, the PLUMED executable and
library will remember where libxdrfile is, without the need to load libxdrfile module at runtime.
Notice that this trick often does not work for fundamental libraries such as C++ and MPI library. As a consequence,
usually the PLUMED module should load the compiler and MPI modules.
diff --git a/user-doc/Introduction.md b/user-doc/Introduction.md
index 5f4a28721811584356e50686b1679f52f58421ad..3b56742b16a2abc6f882a57fb66e6a2f1803d72e 100644
--- a/user-doc/Introduction.md
+++ b/user-doc/Introduction.md
@@ -35,7 +35,9 @@ As far as we know, the following MD codes can be used with PLUMED out of the box
- [IPHIGENIE](http://sourceforge.net/projects/iphigenie/).
- [AceMD](http://www.multiscalelab.org/acemd/), see [this link](https://github.com/tonigi/ACEMD-PLUMED).
- [OpenMM](http://openmm.org), using the [openmmp-plumed plugin](http://github.com/peastman/openmm-plumed).
-- [DL_POLY4](http://www.scd.stfc.ac.uk//research/app/ccg/software/DL_POLY/44516.aspx).
+- [DL_POLY4](https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx).
+- [VNL-ATK](https://quantumwise.com), see [this link](https://docs.quantumwise.com/tutorials/metadynamics_with_plumed/metadynamics_with_plumed.html).
+- [ABIN](https://github.com/PHOTOX/ABIN).
Please refer to the documentation of the MD code to know how to use it with the latest PLUMED release.
If you maintain another MD code that is PLUMED-ready let us know and we will add it to this list.
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 2ad2f9abcac3cc5a5e0fe1798826055d183a64c3..328ace1e1c0ed7519ebdad03977642f0b6c07035 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -2569,8 +2569,8 @@ author = {Bonomi, Massimiliano and Camilloni, Carlo},
title = {{Integrative structural and dynamical biology with PLUMED-ISDB}},
journal = {Bioinformatics},
year = {2017},
-volume = {},
-pages = {},
+volume = {33},
+pages = {3999--4000},
}
@Article{Lelievre2007,
@@ -2698,7 +2698,7 @@ pages = {},
Pages = {773--781},
Publisher = {Curran Associates, Inc., Red Hook, NY},
Title = {Non-strongly-convex smooth stochastic approximation with convergence rate O(1/n)},
- Url = {http://papers.nips.cc/paper/4900-non-strongly-convex-smooth-stochastic-approximation-with-convergence-rate-o1n.pdf}
+ Url = {http://papers.nips.cc/paper/4900-non-strongly-convex-smooth-stochastic-approximation-with-convergence-rate-o1n.pdf},
Year = {2013}
}
diff --git a/user-doc/tutorials/belfast-7.txt b/user-doc/tutorials/belfast-7.txt
index b81abd651fd9751472c1e852a54e96533b9542c3..ef3bf26fa199333c18c54afff28973226d7ba1f0 100644
--- a/user-doc/tutorials/belfast-7.txt
+++ b/user-doc/tutorials/belfast-7.txt
@@ -22,7 +22,7 @@ In PT, exchanges are usually attempted between adjacent temperatures
with the following acceptance probability:
\f[
-p(i \rightarrow j) = min \{ 1,\Delta_{i,j}^{PT} \},
+p(i \rightarrow j) = min \{ 1,e^{\Delta_{i,j}^{PT}} \},
\f]
with
diff --git a/user-doc/tutorials/munster.txt b/user-doc/tutorials/munster.txt
index 1c1745f8fe676a74524ccf643c6440f3bb89b0b4..3595a825d973c740ea089434df311e113e33c7dc 100644
--- a/user-doc/tutorials/munster.txt
+++ b/user-doc/tutorials/munster.txt
@@ -25,8 +25,7 @@ more realistic but slower, and a setup in gas phase, which is much faster.
Simulations are made using GROMACS 4.6.7, which is here assumed to be already patched with PLUMED and properly installed.
However, these examples could be easily converted to other MD software.
-All the gromacs input files and analsys scripts are provided in this
-<a href="tutorial-resources/munster.tar.gz" download="munster.tar.gz"> tarball </a>.
+All the gromacs input files and analsys scripts are provided in this \tarball{munster}.
Users are expected to write PLUMED input files based on the instructions below.