From 4e6818a61f99e66c7b2cedea1c34e39b36702fd5 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 16 Jun 2011 13:20:28 +0200
Subject: [PATCH] Initial version
This is the draft version that I prepared and that we will use as
a starting point. Still it is a bit dirty, and I will try to improve
documentation and delete unused routines
---
.gitignore | 11 +
Makefile | 41 +
README | 16 +
configurations/aix.mpi.xlc | 29 +
configurations/aix.xlc | 29 +
configurations/linux.gcc | 28 +
configurations/linux.icc | 26 +
configurations/linux.mpi.gcc | 27 +
configurations/linux.mpi.icc | 23 +
configurations/linux.pgi | 29 +
configurations/mac.gcc | 33 +
configurations/mac.mpi.gcc | 28 +
configure.sh | 46 +
developer-doc/.gitignore | 4 +
developer-doc/Doc.txt | 295 +++
developer-doc/Doxyfile | 1417 +++++++++++
developer-doc/Makefile | 8 +
extensions/DoNothing.cpp | 27 +
extensions/Makefile | 39 +
imd/.gitignore | 4 +
imd/Makefile | 27 +
include/Plumed.h | 1 +
patches/amber9.config | 6 +
patches/amber9.diff | 268 ++
patches/gromacs-4.0.7.config | 6 +
patches/gromacs-4.0.7.diff | 253 ++
patches/gromacs-4.5.3.config | 6 +
patches/gromacs-4.5.3.diff | 236 ++
patches/namd-2.7.config | 6 +
patches/namd-2.7.diff | 264 ++
patches/patch.sh | 254 ++
src/.gitignore | 2 +
src/Action.cpp | 83 +
src/Action.h | 166 ++
src/ActionAtomistic.cpp | 49 +
src/ActionAtomistic.h | 101 +
src/ActionPilot.cpp | 24 +
src/ActionPilot.h | 25 +
src/ActionRegister.cpp | 59 +
src/ActionRegister.h | 69 +
src/ActionSet.cpp | 15 +
src/ActionSet.h | 79 +
src/ActionSetup.cpp | 15 +
src/ActionSetup.h | 23 +
src/ActionWithArguments.cpp | 65 +
src/ActionWithArguments.h | 49 +
src/ActionWithValue.cpp | 69 +
src/ActionWithValue.h | 74 +
src/Atoms.cpp | 297 +++
src/Atoms.h | 182 ++
src/Bias.cpp | 24 +
src/Bias.h | 40 +
src/BiasMovingRestraint.cpp | 116 +
src/BiasRestraint.cpp | 85 +
src/Colvar.cpp | 61 +
src/Colvar.h | 86 +
src/ColvarDistance.cpp | 119 +
src/ColvarEnergy.cpp | 58 +
src/ColvarTemplate.cpp | 118 +
src/ColvarVolume.cpp | 62 +
src/Debug.cpp | 73 +
src/Flush.cpp | 45 +
src/Function.cpp | 31 +
src/Function.h | 35 +
src/FunctionCombine.cpp | 67 +
src/FunctionMatheval.cpp | 111 +
src/IMD.cpp | 252 ++
src/Log.cpp | 54 +
src/Log.h | 53 +
src/MDAtoms.cpp | 243 ++
src/MDAtoms.h | 44 +
src/Makefile | 85 +
src/Pbc.cpp | 66 +
src/Pbc.h | 21 +
src/Plumed.c | 194 ++
src/Plumed.h | 238 ++
src/PlumedCommunicator.cpp | 119 +
src/PlumedCommunicator.h | 184 ++
src/PlumedConfig.h.in | 12 +
src/PlumedMain.cpp | 442 ++++
src/PlumedMain.h | 135 +
src/PlumedStatic.cpp | 8 +
src/Print.cpp | 109 +
src/Tensor.h | 148 ++
src/Tools.cpp | 117 +
src/Tools.h | 103 +
src/Units.cpp | 133 +
src/Value.cpp | 15 +
src/Value.h | 47 +
src/Vector.cpp | 9 +
src/Vector.h | 110 +
test/Makefile | 15 +
test/amber/.gitignore | 6 +
test/amber/amber_input | 11 +
test/amber/plumed.dat | 4 +
test/amber/system.inpcrd | 13 +
test/amber/system.prmtop | 232 ++
test/gromacs/.gitignore | 6 +
test/gromacs/conf.gro | 652 +++++
test/gromacs/grompp.mdp | 60 +
test/gromacs/plumed.dat | 33 +
test/gromacs/topol.top | 225 ++
test/link/.gitignore | 9 +
test/link/Makefile | 52 +
test/link/main.cpp | 38 +
test/link/mainc.c | 25 +
test/link/mainf.f90 | 14 +
test/link/plumed.dat | 4 +
test/namd/.gitignore | 7 +
test/namd/dia2.pdb | 24 +
test/namd/dia2.psf | 98 +
test/namd/namd_input | 43 +
test/namd/par_all27_prot_lipid.prm | 3681 ++++++++++++++++++++++++++++
test/namd/plumed.dat | 31 +
test/simplemd/.gitignore | 8 +
test/simplemd/Makefile | 37 +
test/simplemd/gasdev.f | 23 +
test/simplemd/in | 10 +
test/simplemd/input.xyz | 110 +
test/simplemd/plumed.dat | 27 +
test/simplemd/ran1.f | 27 +
test/simplemd/routines.f90 | 396 +++
test/simplemd/simplemd.f90 | 204 ++
tools/plumed | 71 +
tools/scripts/newcv.sh | 16 +
user-doc/.gitignore | 6 +
user-doc/Doc.txt | 176 ++
user-doc/Doxyfile | 1649 +++++++++++++
user-doc/Makefile | 9 +
user-doc/extract | 38 +
130 files changed, 17095 insertions(+)
create mode 100644 Makefile
create mode 100644 README
create mode 100644 configurations/aix.mpi.xlc
create mode 100644 configurations/aix.xlc
create mode 100644 configurations/linux.gcc
create mode 100644 configurations/linux.icc
create mode 100644 configurations/linux.mpi.gcc
create mode 100644 configurations/linux.mpi.icc
create mode 100644 configurations/linux.pgi
create mode 100644 configurations/mac.gcc
create mode 100644 configurations/mac.mpi.gcc
create mode 100755 configure.sh
create mode 100644 developer-doc/.gitignore
create mode 100644 developer-doc/Doc.txt
create mode 100644 developer-doc/Doxyfile
create mode 100644 developer-doc/Makefile
create mode 100644 extensions/DoNothing.cpp
create mode 100644 extensions/Makefile
create mode 100644 imd/.gitignore
create mode 100644 imd/Makefile
create mode 120000 include/Plumed.h
create mode 100644 patches/amber9.config
create mode 100644 patches/amber9.diff
create mode 100644 patches/gromacs-4.0.7.config
create mode 100644 patches/gromacs-4.0.7.diff
create mode 100644 patches/gromacs-4.5.3.config
create mode 100644 patches/gromacs-4.5.3.diff
create mode 100644 patches/namd-2.7.config
create mode 100644 patches/namd-2.7.diff
create mode 100755 patches/patch.sh
create mode 100644 src/.gitignore
create mode 100644 src/Action.cpp
create mode 100644 src/Action.h
create mode 100644 src/ActionAtomistic.cpp
create mode 100644 src/ActionAtomistic.h
create mode 100644 src/ActionPilot.cpp
create mode 100644 src/ActionPilot.h
create mode 100644 src/ActionRegister.cpp
create mode 100644 src/ActionRegister.h
create mode 100644 src/ActionSet.cpp
create mode 100644 src/ActionSet.h
create mode 100644 src/ActionSetup.cpp
create mode 100644 src/ActionSetup.h
create mode 100644 src/ActionWithArguments.cpp
create mode 100644 src/ActionWithArguments.h
create mode 100644 src/ActionWithValue.cpp
create mode 100644 src/ActionWithValue.h
create mode 100644 src/Atoms.cpp
create mode 100644 src/Atoms.h
create mode 100644 src/Bias.cpp
create mode 100644 src/Bias.h
create mode 100644 src/BiasMovingRestraint.cpp
create mode 100644 src/BiasRestraint.cpp
create mode 100644 src/Colvar.cpp
create mode 100644 src/Colvar.h
create mode 100644 src/ColvarDistance.cpp
create mode 100644 src/ColvarEnergy.cpp
create mode 100644 src/ColvarTemplate.cpp
create mode 100644 src/ColvarVolume.cpp
create mode 100644 src/Debug.cpp
create mode 100644 src/Flush.cpp
create mode 100644 src/Function.cpp
create mode 100644 src/Function.h
create mode 100644 src/FunctionCombine.cpp
create mode 100644 src/FunctionMatheval.cpp
create mode 100644 src/IMD.cpp
create mode 100644 src/Log.cpp
create mode 100644 src/Log.h
create mode 100644 src/MDAtoms.cpp
create mode 100644 src/MDAtoms.h
create mode 100644 src/Makefile
create mode 100644 src/Pbc.cpp
create mode 100644 src/Pbc.h
create mode 100644 src/Plumed.c
create mode 100644 src/Plumed.h
create mode 100644 src/PlumedCommunicator.cpp
create mode 100644 src/PlumedCommunicator.h
create mode 100644 src/PlumedConfig.h.in
create mode 100644 src/PlumedMain.cpp
create mode 100644 src/PlumedMain.h
create mode 100644 src/PlumedStatic.cpp
create mode 100644 src/Print.cpp
create mode 100644 src/Tensor.h
create mode 100644 src/Tools.cpp
create mode 100644 src/Tools.h
create mode 100644 src/Units.cpp
create mode 100644 src/Value.cpp
create mode 100644 src/Value.h
create mode 100644 src/Vector.cpp
create mode 100644 src/Vector.h
create mode 100644 test/Makefile
create mode 100644 test/amber/.gitignore
create mode 100644 test/amber/amber_input
create mode 100644 test/amber/plumed.dat
create mode 100644 test/amber/system.inpcrd
create mode 100644 test/amber/system.prmtop
create mode 100644 test/gromacs/.gitignore
create mode 100644 test/gromacs/conf.gro
create mode 100644 test/gromacs/grompp.mdp
create mode 100644 test/gromacs/plumed.dat
create mode 100644 test/gromacs/topol.top
create mode 100644 test/link/.gitignore
create mode 100644 test/link/Makefile
create mode 100644 test/link/main.cpp
create mode 100644 test/link/mainc.c
create mode 100644 test/link/mainf.f90
create mode 100644 test/link/plumed.dat
create mode 100644 test/namd/.gitignore
create mode 100644 test/namd/dia2.pdb
create mode 100644 test/namd/dia2.psf
create mode 100644 test/namd/namd_input
create mode 100755 test/namd/par_all27_prot_lipid.prm
create mode 100644 test/namd/plumed.dat
create mode 100644 test/simplemd/.gitignore
create mode 100644 test/simplemd/Makefile
create mode 100644 test/simplemd/gasdev.f
create mode 100644 test/simplemd/in
create mode 100644 test/simplemd/input.xyz
create mode 100644 test/simplemd/plumed.dat
create mode 100644 test/simplemd/ran1.f
create mode 100644 test/simplemd/routines.f90
create mode 100644 test/simplemd/simplemd.f90
create mode 100755 tools/plumed
create mode 100755 tools/scripts/newcv.sh
create mode 100644 user-doc/.gitignore
create mode 100644 user-doc/Doc.txt
create mode 100644 user-doc/Doxyfile
create mode 100644 user-doc/Makefile
create mode 100755 user-doc/extract
diff --git a/.gitignore b/.gitignore
index b25c15b81..e1ddbad05 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,12 @@
+.DS_Store
*~
+*.o
+*.so
+*.dylib
+makefile.dep
+/gromacs*
+/Makefile.conf
+/sourceme.sh
+/tmp
+*.swp
+core
diff --git a/Makefile b/Makefile
new file mode 100644
index 000000000..ea793c482
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,41 @@
+-include Makefile.conf
+
+SUBDIRS = src extensions test
+
+.PHONY: all clean $(SUBDIRS) doc docclean
+
+ifdef GCCDEP
+all: $(SUBDIRS)
+else
+all:
+ @echo No configuration available
+ @echo First run ./configure.sh
+endif
+
+$(SUBDIRS):
+ $(MAKE) -C $@
+
+# compile plumed before tests:
+test: src
+
+clean:
+ cd src && make clean
+ cd extensions && make clean
+ cd test && make clean
+ cd imd && make clean
+ rm -f *~ */*~ */*/*~
+
+fullclean:
+ make clean
+ rm -f Makefile.conf
+ rm -f sourceme.sh
+
+doc:
+ cd user-doc && make
+ cd developer-doc && make
+
+docclean:
+ cd user-doc && make clean
+ cd developer-doc && make clean
+
+
diff --git a/README b/README
new file mode 100644
index 000000000..d497dbf88
--- /dev/null
+++ b/README
@@ -0,0 +1,16 @@
+DOCUMENTATION
+
+To build the documentation, type
+$ make doc
+You need doxygen (www.doxygen.org)
+installed to see the html documentation,
+and graphviz (www.graphviz.org/)
+if you want to see the graphs
+of class hierarichy.
+
+The starting point for user documentation is then
+user-doc/html/index.html
+
+The starting point for developer documentation is
+developer-doc/html/index.html
+
diff --git a/configurations/aix.mpi.xlc b/configurations/aix.mpi.xlc
new file mode 100644
index 000000000..2f7252c44
--- /dev/null
+++ b/configurations/aix.mpi.xlc
@@ -0,0 +1,29 @@
+
+CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+DOUBLEPRECISION=-qrealsize=8
+
+
+LIBS=-ldl
+DYNAMIC_LIBS=$(IMDLIB)
+
+CPPFLAGS=-D__PLUMED_MPI -D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(IMDDEF)
+#CXXFLAGS=-pedantic -Wall -O -fPIC
+#CFLAGS=-pedantic -Wall -O -fPIC
+CXXFLAGS=-O0 -G -qpic -qrtti=all -qlanglvl=strict98 -qlonglong
+CFLAGS=-O0 -qpic
+
+LDFLAGS=-brtl -bdynamic -bexpall
+SOEXT=so
+LDSO=mpCC -G -qmkshrobj -bM:SRE $(CFLAGS)
+LD=mpCC
+LDF90=mpCC -lm -lxlf90
+CXX=mpCC
+CC=mpcc
+FC=mpxlf
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configurations/aix.xlc b/configurations/aix.xlc
new file mode 100644
index 000000000..5ee09575b
--- /dev/null
+++ b/configurations/aix.xlc
@@ -0,0 +1,29 @@
+
+CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+DOUBLEPRECISION=-qrealsize=8
+
+
+LIBS=-ldl
+DYNAMIC_LIBS=$(IMDLIB)
+
+CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(IMDDEF)
+#CXXFLAGS=-pedantic -Wall -O -fPIC
+#CFLAGS=-pedantic -Wall -O -fPIC
+CXXFLAGS=-O0 -G -qpic -qrtti=all
+CFLAGS=-O0 -qpic
+
+LDFLAGS=-brtl -bdynamic -bexpall
+SOEXT=so
+LDSO=xlc++ -G -qmkshrobj -bM:SRE $(CFLAGS)
+LD=xlc++
+LDF90=xlc++ -lm -lxlf90
+CXX=xlc++
+CC=xlc
+FC=xlf
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configurations/linux.gcc b/configurations/linux.gcc
new file mode 100644
index 000000000..67b3b9b05
--- /dev/null
+++ b/configurations/linux.gcc
@@ -0,0 +1,28 @@
+
+#CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+
+LIBS=-ldl
+
+DYNAMIC_LIBS=-lstdc++ $(IMDLIB)
+DOUBLEPRECISION=-fdefault-real-8
+
+
+CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(IMDDEF)
+CXXFLAGS=-pedantic -Wall -O -fPIC -ansi
+CFLAGS=-pedantic -Wall -O -fPIC -ansi
+
+LDFLAGS=-rdynamic
+SOEXT=so
+LDSO=gcc -shared $(CFLAGS)
+LD=g++
+LDF90=gfortran
+CXX=g++
+CC=gcc
+FC=gfortran
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configurations/linux.icc b/configurations/linux.icc
new file mode 100644
index 000000000..b5c15f897
--- /dev/null
+++ b/configurations/linux.icc
@@ -0,0 +1,26 @@
+
+#CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+
+LIBS=-ldl
+DYNAMIC_LIBS=-lstdc++ $(IMDLIB)
+DOUBLEPRECISION=-r8
+
+CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(IMDDEF)
+CXXFLAGS=-O -fPIC -Wall -wd981,383,1418
+CFLAGS=-O -fPIC -Wall
+
+LDFLAGS=-rdynamic
+SOEXT=so
+LDSO=icc -shared $(CFLAGS)
+LD=icpc
+LDF90=ifort
+CXX=icpc
+CC=icc
+FC=ifort
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configurations/linux.mpi.gcc b/configurations/linux.mpi.gcc
new file mode 100644
index 000000000..3893933d6
--- /dev/null
+++ b/configurations/linux.mpi.gcc
@@ -0,0 +1,27 @@
+
+#CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+
+LIBS=-ldl
+DYNAMIC_LIBS=-lstdc++ -lmpi_cxx $(IMDLIB)
+DOUBLEPRECISION=-fdefault-real-8
+
+
+CPPFLAGS=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(IMDDEF)
+CXXFLAGS=-Wall -O -fPIC -ansi
+CFLAGS=-Wall -O -fPIC -ansi
+
+LDFLAGS=-rdynamic
+SOEXT=so
+LDSO=mpicc -shared $(CFLAGS)
+LD=mpic++
+LDF90=mpif90
+CXX=g++
+CC=mpicc
+FC=mpif90
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configurations/linux.mpi.icc b/configurations/linux.mpi.icc
new file mode 100644
index 000000000..1755be23c
--- /dev/null
+++ b/configurations/linux.mpi.icc
@@ -0,0 +1,23 @@
+
+#CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+
+LIBS=-ldl
+DYNAMIC_LIBS=-lstdc++ $(IMDLIB)
+DOUBLEPRECISION=-r8
+
+CPPFLAGS=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(IMDDEF)
+CXXFLAGS=-O -fPIC -Wall -wd981,383,1418
+CFLAGS=-O -fPIC -Wall
+
+LDFLAGS=-rdynamic
+SOEXT=so
+LDSO=mpicc -shared $(CFLAGS)
+LD=mpic++
+LDF90=mpif90
+CXX=mpic++
+CC=mpicc
+FC=mpif90
+
+GCCDEP=mpic++
+
+
diff --git a/configurations/linux.pgi b/configurations/linux.pgi
new file mode 100644
index 000000000..e37338083
--- /dev/null
+++ b/configurations/linux.pgi
@@ -0,0 +1,29 @@
+
+#CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+# NOTE:
+# I did not find the proper compilation flags for dynamic binding
+# moreover, I did not have a f90 license...
+
+LIBS=-ldl -lstdc++
+DOUBLEPRECISION=-fdefault-real-8
+
+
+CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE)
+CXXFLAGS=-O -fPIC
+CFLAGS=-O -fPIC
+
+LDFLAGS=-Bdynamic
+SOEXT=so
+LDSO=pgcc -shared $(CFLAGS)
+LD=pgcpp
+LDF90=pgf90
+CXX=pgcpp
+CC=pgcc
+FC=pgf90
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configurations/mac.gcc b/configurations/mac.gcc
new file mode 100644
index 000000000..5cc866ea6
--- /dev/null
+++ b/configurations/mac.gcc
@@ -0,0 +1,33 @@
+
+CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+DOUBLEPRECISION=-fdefault-real-8
+
+LIBS=-ldl
+DYNAMIC_LIBS=-L/sw/lib -lmatheval -lstdc++ $(IMDLIB)
+
+WARNINGS=-pedantic -Wall -Wextra -Wfloat-equal -Wwrite-strings -Wpointer-arith -Wcast-qual \
+ -Wcast-align -Wconversion -Wshorten-64-to-32 \
+ -Wredundant-decls -Wvariadic-macros -Werror
+
+CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) \
+ -I/sw/include -I/sw/include/openmpi -D__PLUMED_HAS_MATHEVAL $(IMDDEF)
+CXXFLAGS=-O -fPIC $(WARNINGS) -Wstrict-null-sentinel -Wold-style-cast
+CFLAGS=-O -fPIC $(WARNINGS) \
+ -Wdeclaration-after-statement -Wbad-function-cast -Wstrict-prototypes \
+ -Wold-style-definition -Wmissing-prototypes -Wmissing-declarations -Wnested-externs -Wno-int-to-pointer-cast
+
+LDFLAGS=
+SOEXT=dylib
+LDSO=g++ -undefined suppress -flat_namespace -dynamiclib
+LD=g++
+LDF90=gfortran
+CXX=g++
+CC=gcc
+FC=gfortran
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configurations/mac.mpi.gcc b/configurations/mac.mpi.gcc
new file mode 100644
index 000000000..6614b4514
--- /dev/null
+++ b/configurations/mac.mpi.gcc
@@ -0,0 +1,28 @@
+
+CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG
+DOUBLEPRECISION=-fdefault-real-8
+
+
+LIBS=-ldl
+DYNAMIC_LIBS=-L/sw/lib -lmatheval -lmpi_cxx -lmpi_f77 -lstdc++ $(IMDLIB)
+
+CPPFLAGS=-D__PLUMED_MPI -D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) \
+ -D_REENTRANT -I/sw/include -I/sw/include/openmpi -D__PLUMED_HAS_MATHEVAL $(IMDDEF)
+CXXFLAGS=-Wall -O -fPIC
+CFLAGS=-Wall -O -fPIC
+
+LDFLAGS=
+SOEXT=dylib
+LDSO=om-mpic++ -undefined suppress -flat_namespace -dynamiclib
+LD=om-mpic++
+LDF90=om-mpif90
+CXX=om-mpic++
+CC=gcc
+FC=om-mpif90
+
+GCCDEP=g++
+
+
+
+
+
diff --git a/configure.sh b/configure.sh
new file mode 100755
index 000000000..4bb40174e
--- /dev/null
+++ b/configure.sh
@@ -0,0 +1,46 @@
+#! /bin/bash
+
+
+rm -f sourceme.sh Makefile.conf
+
+prefix=""
+case "$(uname)" in
+(Linux) prefix=linux. ;;
+(AIX) prefix=aix. ;;
+(Darwin) prefix=mac. ;;
+esac
+
+conflist=$(cd configurations ; echo $prefix*)
+
+PS3="Choose a configuration:"
+select conf in $conflist
+do
+ [[ -n "$conf" ]] && break
+done
+
+ln -s configurations/$conf Makefile.conf
+
+
+case "$conf" in
+(aix.*)
+ SOEXT=so
+ echo "On cineca, you may need to load the following modules:"
+ echo "module load make"
+ echo "module load sed"
+;;
+(mac.*)
+ SOEXT=dylib
+;;
+(*)
+ SOEXT=so
+esac
+
+echo 'export PATH="$PATH:'"$PWD"'/tools/"' >> sourceme.sh
+# this is just for mac:
+echo 'export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:'"$PWD"'/src/"' >> sourceme.sh
+
+cat << EOF >> sourceme.sh
+export PLUMED_KERNEL="$PWD/src/libplumedKernel.$SOEXT"
+export PLUMED_ROOT="$PWD"
+EOF
+
diff --git a/developer-doc/.gitignore b/developer-doc/.gitignore
new file mode 100644
index 000000000..53e7c03e1
--- /dev/null
+++ b/developer-doc/.gitignore
@@ -0,0 +1,4 @@
+/html
+/latex
+/*.tmp
+
diff --git a/developer-doc/Doc.txt b/developer-doc/Doc.txt
new file mode 100644
index 000000000..b32c83aaa
--- /dev/null
+++ b/developer-doc/Doc.txt
@@ -0,0 +1,295 @@
+// This document is formatted for Doxygen
+/**
+\mainpage A Plumed Clone
+
+\author Giovanni Bussi (as of now)
+\date 2011
+\version 1.9.x
+\warning Very, very unstable
+
+As it can be guessed from the version number, this is a candidate for PLUMED2
+which should be reviewed by a reasonable number the PLUMED developers.
+If it is not accepted as a full package, it can be considered as a repository
+of a few ideas which can be stolen and used in real PLUMED2 development.
+
+If accepted, a possible road map is:
+- 1.99 public release before end of 2011, cloning most PLUMED1 features.
+ It should be usable by (and useful for) developers and people
+ in the community willing to try it.
+- 2.0 public release before mid of 2012, possibly able to superseed completely PLUMED1.
+
+\section Motivation Motivation
+
+- Simpler interface with MD codes. PLUMED should compile by itself as a library,
+ using a proper configure/make procedure, so as to avoid learning all the compilation
+ details of each MD code. Patching a new code should just consist in the insertion of
+ proper function calls and minimal modification to Makefile (to link plumed library),
+ without the need of further hacking inside PLUMED.
+- PLUMED should be easy to extend. Adding a new method/CV should be possible
+ without touching the rest.
+- Other issues:
+ - More friendly units.
+ - More flexible CVs (such as function of other CVs).
+ - Possibility to re-read input.
+
+\section FeaturesAndChanges Features and changes
+
+- Re-designed from scratch, hopefully better.
+- Input is conceptually similar but NON compatible. It is difficult to automatically
+ convert old input files, but we could provide a short transition guide.
+ The new plumed.dat is a sort of script containing a list of actions to be performed at each step.
+ Notable differences in input:
+ - An Action is composed of a line (possibly with continuations) of
+ space-separated words, and corresponds more-or-less to a directive in PLUMED1.
+\verbatim
+DISTANCE ATOMS=0,300 LABEL=dist NOPBC
+\endverbatim
+ The first word (DISTANCE here) defines the directive type, all other words are arguments
+ Most arguments are named, and has the form "NAME=VALUE" (ATOMS and LABEL in the example).
+ Others are flags (NOPBC in the example).
+ - Continuation can be done with "..." syntax (notice the space between DISTANCE and dots):
+\verbatim
+DISTANCE ...
+ ATOMS=0,300
+ LABEL=dist
+ NOPBC
+... DISTANCE
+\endverbatim
+ - All directives can be labeled (LABEL=dist in the example)
+ - A bias can only act on a labeled colvar:
+\verbatim
+DISTANCE ATOMS=0,300 LABEL=dist
+# This is a harmonic restraint
+RESTRAINT ARG=dist KAPPA=1.0 AT=1.0
+\endverbatim
+ - Some colvars have extra named values, which can be accessed with "." syntax
+\verbatim
+DISTANCE ATOMS=1,10 LABEL=dist COMPONENTS
+RESTRAINT ARG=dist.x KAPPA=1.0 AT=1.0
+\endverbatim
+ Here COMPONENTS is telling to DISTANCE to also compute the three components.
+ This is expected to be useful for variables which have multiple components
+ but that are heavy and we would like to compute only once (e.g. components
+ of the inertia tensor of a large molecule).
+ Also methods can have extra named values, such as the energy for a restraint.
+ - to print a COLVAR-like file (name can be changed), use PRINT directive
+\verbatim
+PRINT ARG=d1,d1.x,d1.y,d1.z STRIDE=100 FILE=COLVAR
+# or
+PRINT ARG=d1.* STRIDE=100 FILE=COLVAR1
+# or, to print all the variables defined in the plumed.dat up to this point
+PRINT ARG=* STRIDE=100 FILE=COLVAR_ALL
+\endverbatim
+- The library has been written in C++ for a more flexible structure:
+ - Extensive use of STL containers for things such as lists/vectors/maps/...
+ - Polymorphism for collective variables/free energy methods
+ However, for compatibility, its main interface is in plain C (with FORTRAN
+ and C++ wrappers). All the C++ definitions are hidden in a PLMD namespace.
+- Hierarchy of classes describing each possible Action performed by PLUMED.
+ There is a class for each CV (e.g. PLMD::ColvarDistance, PLMD::ColvarEnergy,
+ PLMD::ColvarVolume), a class for each bias (e.g. PLMD::BiasRestraint, PLMD::BiasMovingRestraint),
+ and a class for each function (e.g. PLMD::FunctionCombine).
+ There are also auxiliary classes to write the output (PLMD::Print),
+ to set the units (PLMD::Units), to print dedug information (PLMD::Debug),
+ to flush the open files (PLMD::Flush), etc.
+ More or less, there should be a class for each possible directive of "plumed.dat".
+ To see the full hierarchy, look at PLMD::Action.
+- It should be possible to program Actions independently from each other. To this
+ aim, there is a register (PLMD::ActionRegister, contained in the function
+ PLMD::actionRegister()) where, during C++ initialization, each
+ Action registers itself. Thus, if a new CV or bias is added, there is no need
+ for recompilation. If dlopen() is available on a system, it should be possible
+ to load Actions runtime (using LOAD directive).
+ In the long run we can imagine libraries of CVs
+ suitable for different problems and, possibly, released independently from
+ the kernel. On a mainframe, one could add CVs without recompiling neither plumed
+ nor the MD engine.
+- There is an option to load the plumed kernel at runtime. If you patch with
+ --runtime, the plumed kernel is looked for at the path in variable PLUMED_KERNEL.
+ If the variable is not set, basic (un-plumed) version of MD is used.
+ On a mainframe, one can have multiple installed plumed versions.
+- Ideally, inside the kernel there is nothing related to specific CVs or FE-methods. Thus, CVs and
+ methods are optional plugins for PLUMED. The only exception
+ are tools which are common to several CVs/methods, such as grid interpolators, etc.
+- Ideally, inside the kernel there is nothing related to specific MD code. The interface is kept
+ as standard as possibly. Anyway, all the details of the interaction PLUMED/MD are inside the
+ src/Atoms.cpp file. E.g., there are two (templated) versionsi of class PLMD::MDAtoms,
+ one for double precision and the other
+ for single precision MD. Code specific tools could be added here. In the future, we may try to
+ design a plugin approach also for MD engines (similarly to CVs/methods).
+- To simplify interface, there is a single routine plumed_cmd which takes a string and a pointer.
+ It can be used to pass any information to plumed, such as:
+\verbatim
+plumed p=plumed_create();
+plumed_cmd(p,"setNatoms",&natoms);
+plumed_cmd(p,"setMDEngine","gromacs");
+plumed_cmd(p,"init",NULL);
+...
+plumed_cmd(plumedmain,"setPositions",pos);
+plumed_cmd(plumedmain,"setBox",box);
+plumed_cmd(plumedmain,"setEnergy",&energy);
+plumed_cmd(plumedmain,"setForces",forces);
+plumed_cmd(plumedmain,"setVirial",virial);
+plumed_cmd(plumedmain,"calc",NULL);
+...
+plumed_finalize(p);
+\endverbatim
+ Fortran/C++ interfaces are similar (see src/Plumed.c for details), and are based on the C interface
+ (wrappers).
+- Units: PLUMED reads and writes only in its internal units, which, by default, are
+ nm and kj/mol. In plumed.dat it is possible to change it to other choices:
+\verbatim
+UNITS ...
+ LENGTH=A
+ TIME=fs
+ ENERGY=kcal/mol
+... UNITS
+\endverbatim
+ The MD code should specify to plumed its internal units, so as to allow proper conversion.
+ E.g., a code using angstrom and kcal should do the following calls
+\verbatim
+double energyUnits=4.184;
+double lengthUnits=0.1;
+plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
+plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
+\endverbatim
+- Other cool features:
+ - Functions of colvars (or functions of functions) can be used. For example, defining:
+\verbatim
+COMBINE LABEL=sum2 ARG=dist.x,dist.y,dist.z POWERS=2,2,2
+COMBINE LABEL=sqrtsum2 ARG=sum2 POWERS=0.5
+# The following two restraints are equivalent:
+RESTRAINT ARG=dist AT=1.2 KAPPA=1.0
+RESTRAINT ARG=sqrtsum2 AT=1.2 KAPPA=1.0
+\endverbatim
+ - Multiple-time-step: biases can be applied with multiple-time-step using a stride. This should
+ help for variables which are heavy to compute but smooth
+\verbatim
+RESTRAINT ARG=dist AT=1.2 KAPPA=1.0 STRIDE=2
+\endverbatim
+ - It is possible to include other files:
+\verbatim
+INCLUDE anotherplumed.dat
+\endverbatim
+ - It is possible to load shared libraries implementing new CVs and methods:
+\verbatim
+LOAD share-object.so
+\endverbatim
+
+
+\section SharingPolicy Sharing Policy
+- I think that Plumed should become fully open, with a public-access shared repository.
+ I would like to switch from cvs to git, which allows for easier branch manipulation.
+ On the central repository, we should have a public master branch where we can
+ publish our work, but for which we do not provide support (developer version).
+ From time to time, as usual, we can provide a supported release (2.0, 2.1 ,...)
+- If it is necessary to work privately, it can be done on a local branch
+ (maybe shared among a few collaborators). Git easily allows to merge multiple times, so it should
+ be relatively easy to stay up do date with the master branch. Finally, when the work
+ is ready, we can merge it into the master branch.
+ This sort of private working should be discouraged for the development of PLUMED kernel.
+ However, it would be perfect to implement new CVs or new methods, since they are
+ completely decoupled from the rest.
+
+\section ToDo To Do
+
+\todo Pbc on COLVARs (possibly with some smart trick for functions-of-functions).
+\todo Optimize atoms sharing. "Calc" should be divided in more steps:
+* Finding list of atoms needed and requesting them (on NAMD, this goes at the
+end of the previous step).
+* Sending the atoms
+* Receiving the atoms and computing everything
+* Sending the forces back
+Moreover, it would be nice to allow PLUMED to be run only on a subset of
+the available processors.
+\todo Replica exchange.
+\todo Interfaces with other codes
+\todo Implementation of CVs
+\todo Implementation of free energy methods
+
+\section Install Install
+
+- Configure and compile your MD code
+- Configure and compile PLUMED, possibly using the same compiler:
+\verbatim
+$ ./configure.sh
+... choose your compiler interactively here ...
+... it may be necessary to edit the Makefile.conf file ...
+$ make -j 4
+\endverbatim
+- Source the ./sourceme.sh file
+\verbatim
+$ source sourceme.sh
+\endverbatim
+ \attention This should be done on every shell where you want to patch/run plumed
+- Go to your MD code directory and do the patch
+\verbatim
+$ plumed patch --patch
+\endverbatim
+ (use -h to get information about other options). Also experiment other linking modes (e.g. --runtime)
+- Recompile your MD code (without necessarily cleaning it)
+
+\section Content Content
+
+src/
+Plumed library source code (C++) plus a two wrapper files (Plumed.c and PlumedStatic.cpp; the latter is just
+equivalent to the former but is compiled as cpp, for testing, and does not allow runtime binding).
+Sources are compiled into a libplumed.so library and a libplumedKernel.so library
+(replace .so with .dylib on Mac).
+The src/Plumed.inc file contains shortcuts for the compilation. Just include it in your makefile and:
+- link the src/Plumed.h file in an included directory
+- add to the linker command the $(PLUMED_LDFLAG) options, to have the proper link flags
+- add to the linker command the $(PLUMED_LIBS) variable, to link the proper external libraries
+- add to the linker command one of the following variables:
+ - (A) \$(PLUMED_OBJ) : plumed will be statically bound
+ - (B) \$(PLUMED_SHARED_OBJ) : plumed will be dynamically bound
+ - (C) \$(PLUMED_WRAPPER) : behavior depend on runtime value of the PLUMED_KERNEL environment variable.
+ If set to the full path of the libplumedKernel.so library, plumed will be available.
+ If unset, or if set to a wrong file, plumed will not be available.
+- The difference between (A) and (B) is that in case (B) if you recompile plumed and rerun MD your code
+ is automatically up to date.
+ The difference between (B) and (C) is that in case (C) the MD code is able to run also if plumed is
+ not available. This allows to have a single compiled MD code for both plumed users and others.
+ Moreover, in case (C) it is trivial to change plumed version at execution time, by properly setting
+ the PLUMED_KERNEL environment variable.
+ Notice that in (B) case the full path of the plumed library is recorded, thus it should not
+ be changed after patching, and it should be reachable from computing nodes.
+ All these task can be done automatically with "plumed patch" using respectively the flags:
+ - (A) --static
+ - (B) --shared
+ - (C) --runtime
+
+extensions/
+ Plumed extensions (e.g. contributed collective variables, ...)
+ They are compiled into a libplumedExtensions.so file which can be loaded at runtime.
+ To load them, use LOAD command inside plumed.dat
+
+test/link/
+ A few simple executables to test compilation/linking
+ Executables are:
+- (A) XXX-static statically linked with src/*.o (except src/Plumed.o)
+- (B) XXX dynamically linked with libplumed.so
+- (C) XXX-dummy statically linked with src/Plumed.o
+
+user-doc/
+ User documentation
+
+developer-doc/
+ Developer documentation
+
+\section Notes Notes
+
+Information about C++
+http://www.parashift.com/c++-faq-lite/
+
+Compiler options to use shared libraries on many architectures:
+http://www.fortran-2000.com/ArnaudRecipes/sharedlib.html
+
+\page HowToAddACollectiveVariable How to add a collective variable
+
+\page HowToAddAFunction How to add a function
+
+\page HowToAddABias How to add a biasing potential
+
+
+*/
diff --git a/developer-doc/Doxyfile b/developer-doc/Doxyfile
new file mode 100644
index 000000000..3a861bd64
--- /dev/null
+++ b/developer-doc/Doxyfile
@@ -0,0 +1,1417 @@
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+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespace are hidden.
+
+EXTRACT_ANON_NSPACES =
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or define consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and defines in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page. This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = NO
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be abled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = Doc.txt ../src
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+
+FILE_PATTERNS =
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# directories that are symbolic links (a Unix filesystem feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output. If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
+# is applied to all files.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = YES
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code. Otherwise they will link to the documentstion.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET =
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = NO
+
+# This tag can be used to set the number of enum values (range [1..20])
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to FRAME, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
+# probably better off using the HTML help feature. Other possible values
+# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
+# and Class Hiererachy pages using a tree view instead of an ordered list;
+# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
+# disables this behavior completely. For backwards compatibility with previous
+# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
+# respectively.
+
+GENERATE_TREEVIEW = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, a4wide, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader. This is useful
+# if you want to understand what is going on. On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all function-like macros that are alone
+# on a line, have an all uppercase name, and do not end with a semicolon. Such
+# function macros are typically used for boiler-plate code, and will confuse
+# the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths or
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option is superseded by the HAVE_DOT option below. This is only a
+# fallback. It is recommended to install and use dot, since it yields more
+# powerful graphs.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS =
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = YES
+
+# By default doxygen will write a font called FreeSans.ttf to the output
+# directory and reference it in all dot files that doxygen generates. This
+# font does not include all possible unicode characters however, so when you need
+# these (or just want a differently looking font) you can specify the font name
+# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# By default doxygen will tell dot to use the output directory to look for the
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a
+# different font using DOT_FONTNAME you can set the path where dot
+# can find it using this tag.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = NO
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are png, jpg, or gif
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is enabled by default, which results in a transparent
+# background. Warning: Depending on the platform used, enabling this option
+# may lead to badly anti-aliased labels on the edges of a graph (i.e. they
+# become hard to read).
+
+DOT_TRANSPARENT = YES
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to the search engine
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE = NO
diff --git a/developer-doc/Makefile b/developer-doc/Makefile
new file mode 100644
index 000000000..58f33798a
--- /dev/null
+++ b/developer-doc/Makefile
@@ -0,0 +1,8 @@
+
+.PHONY: all clean
+
+all:
+ doxygen
+
+clean:
+ rm -fr html latex *~
diff --git a/extensions/DoNothing.cpp b/extensions/DoNothing.cpp
new file mode 100644
index 000000000..23ce08409
--- /dev/null
+++ b/extensions/DoNothing.cpp
@@ -0,0 +1,27 @@
+#include "../src/ActionRegister.h"
+#include "../src/ActionSetup.h"
+
+using namespace std;
+
+namespace PLMD{
+
+/// Action which does nothing
+///
+/// It is here to test linking of external libraries
+class DoNothing:
+ public ActionSetup
+{
+public:
+ DoNothing(const ActionOptions&ao);
+};
+
+PLUMED_REGISTER_ACTION(DoNothing,"DONOTHING")
+
+DoNothing::DoNothing(const ActionOptions&ao):
+Action(ao),
+ActionSetup(ao)
+{
+}
+
+}
+
diff --git a/extensions/Makefile b/extensions/Makefile
new file mode 100644
index 000000000..480274527
--- /dev/null
+++ b/extensions/Makefile
@@ -0,0 +1,39 @@
+
+-include ../Makefile.conf
+
+SRC=$(wildcard *.cpp)
+
+OBJ=$(SRC:.cpp=.o)
+SOBJ=$(SRC:.cpp=.$(SOEXT))
+
+.PHONY: all clean
+
+ifdef GCCDEP
+all: libplumedExtensions.$(SOEXT) $(SOBJ)
+else
+all:
+ @echo No configuration available
+ @echo First run ./configure.sh in the root directory
+endif
+
+
+libplumedExtensions.$(SOEXT): $(OBJ)
+ $(LDSO) -o $@ $^
+
+clean:
+ rm -f makefile.dep
+ rm -f *.o
+ifdef SOEXT
+ rm -f *.$(SOEXT)
+endif
+
+makefile.dep : $(SRC) *.h
+ifdef GCCDEP
+ for i in $(ALL_SRC) ; do $(GCCDEP) $(CPPFLAGS) -MM "$${i}"; done > $@
+endif
+
+%.$(SOEXT) : %.o
+ $(LDSO) -o $@ $^
+
+-include makefile.dep
+
diff --git a/imd/.gitignore b/imd/.gitignore
new file mode 100644
index 000000000..a5a5805b5
--- /dev/null
+++ b/imd/.gitignore
@@ -0,0 +1,4 @@
+/*.c
+/*.h
+/Makefile.conf
+/imdapi*
diff --git a/imd/Makefile b/imd/Makefile
new file mode 100644
index 000000000..b112725f5
--- /dev/null
+++ b/imd/Makefile
@@ -0,0 +1,27 @@
+-include ../Makefile.conf
+
+all: Makefile.conf libimd.$(SOEXT)
+
+Makefile.conf: libimd.$(SOEXT)
+ echo IMDLIB=-L$(PWD) -limd > Makefile.conf
+ echo IMDDEF=-D__PLUMED_HAS_IMD >> Makefile.conf
+
+
+libimd.$(SOEXT): imd.o vmdsock.o
+ $(LDSO) -o $@ $^ -lnsl
+
+vmdsock.c imd.c vmdsock.h imd.h: imdapi.tar.gz
+ tar xzOf imdapi.tar.gz imdapi/$@ > $@
+
+vmdsock.o imd.o: vmdsock.h imd.h
+
+imdapi.tar.gz:
+ wget http://www.ks.uiuc.edu/Research/vmd/imd/code/imdapi.tar.gz
+
+
+clean:
+ rm -fr imdapi.tar.gz *.c *.h *.$(SOEXT) Makefile.conf *.o
+
+
+
+
diff --git a/include/Plumed.h b/include/Plumed.h
new file mode 120000
index 000000000..04e460f19
--- /dev/null
+++ b/include/Plumed.h
@@ -0,0 +1 @@
+../src/Plumed.h
\ No newline at end of file
diff --git a/patches/amber9.config b/patches/amber9.config
new file mode 100644
index 000000000..4c6521984
--- /dev/null
+++ b/patches/amber9.config
@@ -0,0 +1,6 @@
+
+
+function plumed_preliminary_test(){
+# check if the README contains the word AMBER and if amber has been already configured
+ grep -q AMBER README 1>/dev/null 2>/dev/null && test -f src/config.h
+}
diff --git a/patches/amber9.diff b/patches/amber9.diff
new file mode 100644
index 000000000..814bd8bc5
--- /dev/null
+++ b/patches/amber9.diff
@@ -0,0 +1,268 @@
+patch -u -l -b -F 5 --suffix=.preplumed "./src/sander/Makefile" << \EOF_EOF
+--- ./src/sander/Makefile.preplumed
++++ ./src/sander/Makefile
+@@ -18,10 +18,11 @@
+ #************************************************************************
+ #
+ # Makefile for Amber 9 SANDER
+ #
+ include ../config.h
++include ../../Plumed.inc
+
+ # Sander Fortran source files are free format
+ LOCALFLAGS = $(FREEFORMAT_FLAG)
+
+ SHELL=/bin/sh
+@@ -169,48 +170,48 @@
+ nxtsec lapack blas lmod divcon checkserconf
+ $(LOAD) -o sander$(SFX) $(MMOBJ) $(QMOBJ) $(QM2OBJ) $(QMMMOBJ_DFTB) \
+ qm_div.o force.o \
+ ../lmod/lmod.a ../dcqtp/src/qmmm/libdivcon.a \
+ ../lapack/lapack.a ../blas/blas.a \
+- ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB)
++ ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB) $(PLUMED_LOAD)
+
+ #---------------------------------------------------------------------------
+ sander.MPI$(SFX): $(NETCDF) $(MMOBJ) $(QMOBJ) $(QM2OBJ) $(QMMMOBJ_DFTB) \
+ qm_div.o force.o \
+ syslib nxtsec lapack blas lmod checkparconf
+ $(LOAD) -o sander.MPI$(SFX) $(MMOBJ) $(QMOBJ) $(QM2OBJ) $(QMMMOBJ_DFTB) \
+ qm_div.o force.o \
+ ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
+- ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB)
++ ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB) $(PLUMED_LOAD)
+
+ #---------------------------------------------------------------------------
+ sander.LES$(SFX): $(NETCDF) $(LESOBJ) syslib nxtsec lapack blas lmod \
+ checkserconf
+ $(LOAD) -o sander.LES$(SFX) $(LESOBJ) \
+ ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
+- ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB)
++ ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB) $(PLUMED_LOAD)
+
+ #---------------------------------------------------------------------------
+ sander.LES.MPI$(SFX): $(NETCDF) $(LESOBJ) syslib nxtsec lapack blas lmod \
+ checkparconf
+ $(LOAD) -o sander.LES.MPI$(SFX) $(LESOBJ) \
+ ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
+- ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB)
++ ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB) $(PLUMED_LOAD)
+
+ #---------------------------------------------------------------------------
+ sander.PIMD$(SFX): $(NETCDF) $(PIMDOBJ) $(EVBPIMD) syslib nxtsec lapack blas \
+ lmod checkserconf
+ $(LOAD) -o sander.PIMD$(SFX) $(PIMDOBJ) $(EVBPIMD) \
+ ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
+- ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB)
++ ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB) $(PLUMED_LOAD)
+
+ #---------------------------------------------------------------------------
+ sander.PIMD.MPI$(SFX): $(NETCDF) $(PIMDOBJ) $(EVBPIMD) syslib nxtsec lapack \
+ blas lmod checkparconf
+ $(LOAD) -o sander.PIMD.MPI$(SFX) $(PIMDOBJ) $(EVBPIMD) \
+ ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
+- ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB)
++ ../lib/nxtsec.o ../lib/sys.a $(NETCDFLIB) $(LOADLIB) $(PLUMED_LOAD)
+
+ #---------------------------------------------------------------------------
+ psander$(SFX): $(NETCDF) $(PSOBJ) $(QMOBJ) $(QM2OBJ) $(QMMMOBJ_DFTB) \
+ qm_div.o force.PS.o syslib \
+ syslib nxtsec lapack blas lmod
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/sander/mdread.f" << \EOF_EOF
+--- ./src/sander/mdread.f.preplumed
++++ ./src/sander/mdread.f
+@@ -78,11 +78,11 @@
+ cut_inner,icfe,clambda,klambda, rbornstat,lastrst,lastist, &
+ itgtmd,tgtrmsd,tgtmdfrc,tgtfitmask,tgtrmsmask, &
+ idecomp,temp0les,restraintmask,restraint_wt,bellymask, &
+ noshakemask, &
+ mmtsb_switch, mmtsb_iterations,rdt,icnstph,solvph,ntcnstph, &
+- ifqnt,ievb, &
++ ifqnt,ievb,plumed,plumedfile, &
+ #ifdef PIMD
+ pimd_runtype, pimd_use_original_mass, ineb, &
+ #endif
+ dtemp, dxm, heat, timlim !all retired
+
+@@ -129,10 +129,13 @@
+ ig = 71277
+ tempi = ZERO
+ ntb = 1
+ ntt = 0
+ temp0 = 300.0d0
++ plumed = 0
++ plumedfile = 'plumed.dat'
++
+ #if defined(LES) || defined(PIMD)
+
+ ! alternate temp for LES copies, if negative then use single bath
+ ! single bath not the same as 2 baths with same target T
+
+@@ -306,10 +309,15 @@
+ else
+ write(6, '(1x,a,/)') 'Could not find cntrl namelist'
+ call mexit(6,1)
+ end if
+
++ if (plumed.eq.1) then
++ write(6, '(1x,a,/)') 'PLUMED is on'
++ write(6, '(1x,a,a,/)') 'PLUMEDfile is ',plumedfile
++ endif
++
+ if (ifqnt>0) then
+ qmmm_nml%ifqnt = .true.
+ if (saltcon /= 0.0d0) then
+ qm_gb%saltcon_on = .true.
+ else
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/sander/md.h" << \EOF_EOF
+--- ./src/sander/md.h.preplumed
++++ ./src/sander/md.h
+@@ -15,22 +15,23 @@
+ ibgwat,ienwat,iorwat, &!36
+ iwatpr,nsolw,igb,alpb,iyammp, &!41
+ gbsa,vrand,iwrap,nrespa,irespa,nrespai,icfe, &!48
+ rbornstat,ivcap,iconstreff, &!51
+ neb,vv,tmode,ipol,iesp,ievb,nodeid,num_noshake, &!59
+- idecomp,icnstph,ntcnstph,maxdup,numexchg,repcrd,numwatkeep !66
+-parameter (BC_MDI=66)
++ idecomp,icnstph,ntcnstph,maxdup,numexchg,repcrd,numwatkeep,& !66
++ plumed !67
++parameter (BC_MDI=67)
+
+ common/mdi/nrp,nspm,ig, &
+ ntx,ntcx,ntxo,ntt,ntp,ntr,init,ntcm,nscm, &
+ isolvp,nsolut,ntc,ntcc,ntf,ntid,ntn,ntnb,nsnb,ndfmin, &
+ nstlim,nrc,ntrx,npscal,imin,maxcyc,ncyc,ntmin, &
+ irest,jfastw,ibgwat,ienwat,iorwat, &
+ iwatpr,nsolw,igb,alpb,iyammp,gbsa,vrand,numexchg,repcrd,numwatkeep, &
+ iwrap,nrespa,irespa,nrespai,icfe,rbornstat, &
+ ivcap,iconstreff,idecomp,klambda,icnstph,ntcnstph,maxdup,neb,vv, &
+- tmode,ipol,iesp,ievb,nodeid,num_noshake
++ tmode,ipol,iesp,ievb,nodeid,num_noshake, plumed
+
+ ! ... floats:
+
+ _REAL_ t,dt,temp0,tautp,pres0,comp,taup,temp,tempi, & !9
+ tol,taur,dx0,drms,vlimit,rbtarg(9),tmass,tmassinv, & !25
+@@ -47,11 +48,12 @@
+ v11,v12,v22,kevb,evbt,Arad
+
+ ! ... strings:
+
+ character(len=4) iwtnm,iowtnm,ihwtnm
+-character(len=256) restraintmask,bellymask,tgtfitmask,tgtrmsmask,noshakemask
++character(len=256) restraintmask,bellymask,tgtfitmask,tgtrmsmask,noshakemask, &
++ plumedfile
+ common/mds/ restraintmask,bellymask,tgtfitmask,tgtrmsmask,noshakemask, &
+- iwtnm,iowtnm,ihwtnm(2)
++ iwtnm,iowtnm,ihwtnm(2),plumedfile
+
+ !-------------END md.h ------------------------------------------------
+
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/sander/sander.f" << \EOF_EOF
+--- ./src/sander/sander.f.preplumed
++++ ./src/sander/sander.f
+@@ -509,10 +509,13 @@
+ !----- Set up integer stack initial size --------------
+ call mpi_bcast(lastist,1,mpi_integer,0,commsander,ierr)
+ call mpi_bcast(lastrst,1,mpi_integer,0,commsander,ierr)
+
+ call stack_setup()
++
++ call mpi_bcast(plumed,1,MPI_INTEGER,0,commsander,ierr)
++ call mpi_bcast(plumedfile,256,MPI_CHARACTER,0,commsander,ierr)
+
+ call mpi_barrier(commsander,ierr)
+ ! ---allocate memory on the non-master nodes:
+
+ if( .not.master ) then
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/sander/runmd.f" << \EOF_EOF
+--- ./src/sander/runmd.f.preplumed
++++ ./src/sander/runmd.f
+@@ -172,10 +172,12 @@
+ character(len=4) prndiptest
+ !--- END VARIABLES FOR DIPOLE PRINTING ---
+
+ _REAL_,parameter :: pressure_constant = 6.85695d+4
+
++ _REAL_ :: energyUnits,timeUnits,lengthUnits
++
+ ! Runmd operates in kcal/mol units for energy, amu for masses,
+ ! and angstoms for distances. To convert the input time parameters
+ ! from picoseconds to internal units, multiply by 20.455
+ ! (which is 10.0*sqrt(4.184)).
+
+@@ -477,10 +479,41 @@
+ ener(9) = box(3)
+
+ ekcmt(1:4) = 0.d0
+ nitp = 0
+ nits = 0
++
++ ! init PLUMED
++ if(plumed.eq.1) then
++ call plumed_g_create()
++ energyUnits=4.184
++ lengthUnits=0.1
++ timeUnits=1.0
++ call plumed_g_cmd("setMDEnergyUnits"//char(0),energyUnits)
++ call plumed_g_cmd("setMDLengthUnits"//char(0),lengthUnits)
++ call plumed_g_cmd("setMDTimeUnits"//char(0),timeUnits)
++ call plumed_g_cmd("setPlumedDat"//char(0),trim(adjustl(plumedfile))//char(0))
++ call plumed_g_cmd("setNatoms"//char(0),nr)
++ call plumed_g_cmd("setMDEngine"//char(0),"amber");
++ call plumed_g_cmd("setTimestep"//char(0),dt);
++# ifdef MPI
++ call plumed_g_cmd("setMPIFComm"//char(0),MPI_COMM_WORLD)
++# endif
++
++ call plumed_g_cmd("init"//char(0),0);
++
++
++! if(ifbox/=0 .and. ifbox/=1 .and. ifbox/=2) then
++! write (6,*) "!!!!! PLUMED ERROR: Only orthorhombic and truncted octahedron cells are supported in this release."
++! write (6,*) "!!!!! ABORTING RUN"
++! stop
++! endif
++! call init_metadyn(nr,dt,amass,xx(l15),ifbox,0,trim(adjustl(plumedfile))//char(0))
++ continue
++ endif
++ ! end init PLUMED
++
+
+ !=======================================================================
+ ! ----- MAKE A FIRST DYNAMICS STEP -----
+ !=======================================================================
+ ! init = 3: general startup if not continuing a previous run
+@@ -815,10 +848,26 @@
+ ! TIME_force is started and stopped inside force
+ call force(xx,ix,ih,ipairs,x,f,ener(23),vir, &
+ xx(l96),xx(l97),xx(l98),xx(l99), qsetup,qpsander, &
+ do_list_update)
+
++ !PLUMED force added
++ if(plumed.eq.1) then
++ call plumed_g_cmd("setStep"//char(0),nstep)
++ call plumed_g_cmd("setPositions"//char(0),x)
++ call plumed_g_cmd("setMasses"//char(0),amass)
++ call plumed_g_cmd("setCharges"//char(0),xx(l15))
++ call plumed_g_cmd("setEnergy"//char(0),ener(23))
++ call plumed_g_cmd("setForces"//char(0),f)
++! call plumed_g_cmd("setVirial",&force_vir[0][0]);
++! call plumed_g_cmd("setBox"//char(0),box)
++ call plumed_g_cmd("calc"//char(0),0);
++
++ end if
++ !PLUMED end
++
++
+ ! Constant pH transition evaluation
+ if ((icnstph /= 0) .and. (mod(irespa,ntcnstph) == 0)) then
+ call cnstphendstep(ix(icpstinf),ix(icpresst),ix(icpptcnt), &
+ ix(icptrsct), xx(lcpene),xx(lcpcrg),xx(l190),xx(l15),ener(39), &
+ icpselres,icpselstat,cnstph_rand_gen)
+EOF_EOF
diff --git a/patches/gromacs-4.0.7.config b/patches/gromacs-4.0.7.config
new file mode 100644
index 000000000..59497e353
--- /dev/null
+++ b/patches/gromacs-4.0.7.config
@@ -0,0 +1,6 @@
+
+
+function plumed_preliminary_test(){
+# check if the README contains the word GROMACS and if gromacs has been already configured
+ grep -q GROMACS README 1>/dev/null 2>/dev/null && test -f src/kernel/Makefile
+}
diff --git a/patches/gromacs-4.0.7.diff b/patches/gromacs-4.0.7.diff
new file mode 100644
index 000000000..62540519a
--- /dev/null
+++ b/patches/gromacs-4.0.7.diff
@@ -0,0 +1,253 @@
+patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/Makefile" << \EOF_EOF
+--- ./src/kernel/Makefile.preplumed
++++ ./src/kernel/Makefile
+@@ -15,10 +15,11 @@
+
+
+ # Note: Makefile is automatically generated from Makefile.in by the configure
+ # script, and Makefile.in is generated from Makefile.am by automake.
+
++include ../../Plumed.inc
+
+
+ pkgdatadir = $(datadir)/gromacs
+ pkglibdir = $(libdir)/gromacs
+ pkgincludedir = $(includedir)/gromacs
+@@ -84,11 +85,11 @@
+ ../gmxlib/libgmx_mpi_d.la
+ am_mdrun_OBJECTS = glaasje.$(OBJEXT) gctio.$(OBJEXT) ionize.$(OBJEXT) \
+ do_gct.$(OBJEXT) repl_ex.$(OBJEXT) xutils.$(OBJEXT) \
+ md.$(OBJEXT) mdrun.$(OBJEXT) genalg.$(OBJEXT)
+ mdrun_OBJECTS = $(am_mdrun_OBJECTS)
+-mdrun_LDADD = $(LDADD)
++mdrun_LDADD = $(LDADD) $(PLUMED_LOAD)
+ mdrun_DEPENDENCIES = $(noinst_LTLIBRARIES) \
+ ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la
+ am_pdb2gmx_OBJECTS = pdb2gmx.$(OBJEXT)
+ pdb2gmx_OBJECTS = $(am_pdb2gmx_OBJECTS)
+ pdb2gmx_LDADD = $(LDADD)
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
+--- ./src/kernel/md.c.preplumed
++++ ./src/kernel/md.c
+@@ -81,10 +81,17 @@
+ #include "compute_io.h"
+ #include "mvdata.h"
+ #include "checkpoint.h"
+ #include "mtop_util.h"
+
++/* PLUMED */
++#include "../../Plumed.h"
++extern int plumedswitch;
++extern plumed plumedmain;
++/* END PLUMED */
++
++
+ #ifdef GMX_MPI
+ #include <mpi.h>
+ #endif
+
+ /* The following two variables and the signal_handler function
+@@ -831,10 +838,41 @@
+ snew(scale_tot,1);
+ } else {
+ scale_tot = NULL;
+ }
+
++/* PLUMED */
++ if(plumedswitch){
++
++ if(PAR(cr)){
++ if(DOMAINDECOMP(cr)) {
++ plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
++ }else{
++ plumed_cmd(plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
++ }
++ }
++
++ plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
++ plumed_cmd(plumedmain,"setMDEngine","gromacs");
++ plumed_cmd(plumedmain,"setLog",fplog);
++ plumed_cmd(plumedmain,"setTimestep",&ir->delta_t);
++
++ plumed_cmd(plumedmain,"init",NULL);
++
++ if(PAR(cr)){
++ if(DOMAINDECOMP(cr)) {
++ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
++ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
++ }else{
++ plumed_cmd(plumedmain,"setAtomsNlocal",&mdatoms->homenr);
++ plumed_cmd(plumedmain,"setAtomsContiguous",&mdatoms->start);
++ }
++ }
++ }
++/* END PLUMED */
++
++
+ /* Write start time */
+ start_t=print_date_and_time(fplog,cr->nodeid,"Started mdrun");
+ wallcycle_start(wcycle,ewcRUN);
+ if (fplog)
+ fprintf(fplog,"\n");
+@@ -1068,10 +1106,16 @@
+ dd_partition_system(fplog,step,cr,bMasterState,
+ state_global,top_global,ir,
+ state,&f,&buf,mdatoms,top,fr,vsite,shellfc,constr,
+ nrnb,wcycle,do_verbose);
+ wallcycle_stop(wcycle,ewcDOMDEC);
++/* PLUMED */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
++ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
++ }
++/* END PLUMED */
+ }
+ }
+
+ if (MASTER(cr) && do_log && !bFFscan)
+ print_ebin_header(fplog,step,t,state->lambda);
+@@ -1128,17 +1172,39 @@
+ else {
+ /* The coordinates (x) are shifted (to get whole molecules) in do_force
+ * This is parallellized as well, and does communication too.
+ * Check comments in sim_util.c
+ */
++
++/* PLUMED */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setStep",&step);
++ plumed_cmd(plumedmain,"setPositions",&state->x[mdatoms->start][0]);
++ plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[mdatoms->start]);
++ plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[mdatoms->start]);
++ plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
++ plumed_cmd(plumedmain,"prepareCalc",NULL);
++ }
++/* END PLUMED */
++
+ do_force(fplog,cr,ir,step,nrnb,wcycle,top,groups,
+ state->box,state->x,&state->hist,
+ f,buf,force_vir,mdatoms,enerd,fcd,
+ state->lambda,graph,
+ fr,vsite,mu_tot,t,fp_field,ed,
+ GMX_FORCE_STATECHANGED | (bNS ? GMX_FORCE_NS : 0) |
+ GMX_FORCE_ALLFORCES);
++
++/* PLUMED */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
++ plumed_cmd(plumedmain,"setForces",&f[mdatoms->start][0]);
++ plumed_cmd(plumedmain,"setVirial",&force_vir[0][0]);
++ plumed_cmd(plumedmain,"performCalc",NULL);
++ }
++/* END PLUMED */
++
+ }
+
+ GMX_BARRIER(cr->mpi_comm_mygroup);
+
+ if (bTCR)
+@@ -1603,10 +1669,17 @@
+ if (DOMAINDECOMP(cr)) {
+ dd_partition_system(fplog,step,cr,TRUE,
+ state_global,top_global,ir,
+ state,&f,&buf,mdatoms,top,fr,vsite,shellfc,constr,
+ nrnb,wcycle,FALSE);
++/* PLUMED */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
++ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
++ }
++/* END PLUMED */
++
+ } else {
+ bcast_state(cr,state,FALSE);
+ }
+ }
+
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/mdrun.c" << \EOF_EOF
+--- ./src/kernel/mdrun.c.preplumed
++++ ./src/kernel/mdrun.c
+@@ -51,10 +51,16 @@
+ #include "checkpoint.h"
+
+ /* afm stuf */
+ #include "pull.h"
+
++/* PLUMED */
++#include "../../Plumed.h"
++int plumedswitch;
++plumed plumedmain;
++/* END PLUMED */
++
+ int main(int argc,char *argv[])
+ {
+ static char *desc[] = {
+ "The mdrun program is the main computational chemistry engine",
+ "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
+@@ -274,11 +280,12 @@
+ { efXVG, "-devout", "deviatie", ffOPTWR },
+ { efXVG, "-runav", "runaver", ffOPTWR },
+ { efXVG, "-px", "pullx", ffOPTWR },
+ { efXVG, "-pf", "pullf", ffOPTWR },
+ { efMTX, "-mtx", "nm", ffOPTWR },
+- { efNDX, "-dn", "dipole", ffOPTWR }
++ { efNDX, "-dn", "dipole", ffOPTWR },
++ { efDAT, "-plumed", "plumed", ffOPTRD } /* PLUMED */
+ };
+ #define NFILE asize(fnm)
+
+ /* Command line options ! */
+ static bool bCart = FALSE;
+@@ -490,17 +497,49 @@
+ ed=NULL;
+
+ ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
+ ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
+ ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
++
++/* PLUMED */
++ plumedswitch=0;
++ if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
++ if(plumedswitch){
++ int plumed_is_there=0;
++ int real_precision=sizeof(real);
++ real energyUnits=1.0;
++ real lengthUnits=1.0;
++ real timeUnits=1.0;
++
++ plumed_installed(&plumed_is_there);
++ if(!plumed_is_there){
++ gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
++ }
++ plumedmain=plumed_create();
++ plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
++// this is not necessary for gromacs units:
++ plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
++ plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
++ plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
++//
++ plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
++ plumedswitch=1;
++ }
++/* END PLUMED */
+
+ mdrunner(fplog,cr,NFILE,fnm,bVerbose,bCompact,
+ ddxyz,dd_node_order,rdd,rconstr,
+ dddlb_opt[0],dlb_scale,ddcsx,ddcsy,ddcsz,
+ nstepout,ed,repl_ex_nst,repl_ex_seed,pforce,
+ cpt_period,max_hours,Flags);
+
++/* PLUMED */
++ if(plumedswitch){
++ plumed_finalize(plumedmain);
++ }
++/* END PLUMED */
++
+ if (gmx_parallel_env)
+ gmx_finalize(cr);
+
+ if (MULTIMASTER(cr)) {
+ thanx(stderr);
+EOF_EOF
diff --git a/patches/gromacs-4.5.3.config b/patches/gromacs-4.5.3.config
new file mode 100644
index 000000000..59497e353
--- /dev/null
+++ b/patches/gromacs-4.5.3.config
@@ -0,0 +1,6 @@
+
+
+function plumed_preliminary_test(){
+# check if the README contains the word GROMACS and if gromacs has been already configured
+ grep -q GROMACS README 1>/dev/null 2>/dev/null && test -f src/kernel/Makefile
+}
diff --git a/patches/gromacs-4.5.3.diff b/patches/gromacs-4.5.3.diff
new file mode 100644
index 000000000..f5da3ceb6
--- /dev/null
+++ b/patches/gromacs-4.5.3.diff
@@ -0,0 +1,236 @@
+patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/Makefile" << \EOF_EOF
+--- ./src/kernel/Makefile.preplumed
++++ ./src/kernel/Makefile
+@@ -16,10 +16,11 @@
+
+
+ # Note: Makefile is automatically generated from Makefile.in by the configure
+ # script, and Makefile.in is generated from Makefile.am by automake.
+
++include ../../Plumed.inc
+
+
+
+ pkgdatadir = $(datadir)/gromacs
+ pkgincludedir = $(includedir)/gromacs
+@@ -141,11 +142,11 @@
+ am_mdrun_OBJECTS = gctio.$(OBJEXT) ionize.$(OBJEXT) do_gct.$(OBJEXT) \
+ repl_ex.$(OBJEXT) xutils.$(OBJEXT) runner.$(OBJEXT) \
+ md.$(OBJEXT) mdrun.$(OBJEXT) genalg.$(OBJEXT) \
+ md_openmm.$(OBJEXT)
+ mdrun_OBJECTS = $(am_mdrun_OBJECTS)
+-mdrun_LDADD = $(LDADD)
++mdrun_LDADD = $(LDADD) $(PLUMED_LOAD)
+ mdrun_DEPENDENCIES = $(lib_LTLIBRARIES) ../mdlib/libmd_mpi_d.la \
+ ../gmxlib/libgmx_mpi_d.la
+ pdb2gmx_SOURCES = pdb2gmx.c
+ pdb2gmx_OBJECTS = pdb2gmx.$(OBJEXT)
+ pdb2gmx_LDADD = $(LDADD)
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/md.c" << \EOF_EOF
+--- ./src/kernel/md.c.preplumed
++++ ./src/kernel/md.c
+@@ -88,10 +88,16 @@
+ #include "mvdata.h"
+ #include "checkpoint.h"
+ #include "mtop_util.h"
+ #include "sighandler.h"
+
++/* PLUMED */
++#include "../../Plumed.h"
++extern int plumedswitch;
++extern plumed plumedmain;
++/* END PLUMED */
++
+ #ifdef GMX_LIB_MPI
+ #include <mpi.h>
+ #endif
+ #ifdef GMX_THREADS
+ #include "tmpi.h"
+@@ -1522,10 +1528,41 @@
+ }
+ }
+ fprintf(fplog,"\n");
+ }
+
++/* PLUMED */
++ if(plumedswitch){
++
++ if(PAR(cr)){
++ if(DOMAINDECOMP(cr)) {
++ plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
++ }else{
++ plumed_cmd(plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
++ }
++ }
++
++ plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
++ plumed_cmd(plumedmain,"setMDEngine","gromacs");
++ plumed_cmd(plumedmain,"setLog",fplog);
++ plumed_cmd(plumedmain,"setTimestep",&ir->delta_t);
++
++ plumed_cmd(plumedmain,"init",NULL);
++
++ if(PAR(cr)){
++ if(DOMAINDECOMP(cr)) {
++ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
++ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
++ }else{
++ plumed_cmd(plumedmain,"setAtomsNlocal",&mdatoms->homenr);
++ plumed_cmd(plumedmain,"setAtomsContiguous",&mdatoms->start);
++ }
++ }
++ }
++/* END PLUMED */
++
++
+ /* Set and write start time */
+ runtime_start(runtime);
+ print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime);
+ wallcycle_start(wcycle,ewcRUN);
+ if (fplog)
+@@ -1802,10 +1839,17 @@
+ state,&f,mdatoms,top,fr,
+ vsite,shellfc,constr,
+ nrnb,wcycle,do_verbose);
+ wallcycle_stop(wcycle,ewcDOMDEC);
+ /* If using an iterative integrator, reallocate space to match the decomposition */
++/* PLUMED */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
++ plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
++ }
++/* END PLUMED */
++
+ }
+ }
+
+ if (MASTER(cr) && do_log && !bFFscan)
+ {
+@@ -1928,16 +1972,37 @@
+ * in do_force.
+ * This is parallellized as well, and does communication too.
+ * Check comments in sim_util.c
+ */
+
++
++ /* PLUMED */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setStep",&step);
++ plumed_cmd(plumedmain,"setPositions",&state->x[mdatoms->start][0]);
++ plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[mdatoms->start]);
++ plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[mdatoms->start]);
++ plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
++ plumed_cmd(plumedmain,"prepareCalc",NULL);
++ }
++ /* END PLUMED */
++
+ do_force(fplog,cr,ir,step,nrnb,wcycle,top,top_global,groups,
+ state->box,state->x,&state->hist,
+ f,force_vir,mdatoms,enerd,fcd,
+ state->lambda,graph,
+ fr,vsite,mu_tot,t,outf->fp_field,ed,bBornRadii,
+ (bNS ? GMX_FORCE_NS : 0) | force_flags);
++ /* PLUMED */
++ if(plumedswitch){
++ plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
++ plumed_cmd(plumedmain,"setForces",&f[mdatoms->start][0]);
++ plumed_cmd(plumedmain,"setVirial",&force_vir[0][0]);
++ plumed_cmd(plumedmain,"performCalc",NULL);
++ }
++ /* END PLUMED */
++
+ }
+
+ GMX_BARRIER(cr->mpi_comm_mygroup);
+
+ if (bTCR)
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/kernel/mdrun.c" << \EOF_EOF
+--- ./src/kernel/mdrun.c.preplumed
++++ ./src/kernel/mdrun.c
+@@ -54,10 +54,16 @@
+ #endif
+
+ /* afm stuf */
+ #include "pull.h"
+
++/* PLUMED */
++#include "../../Plumed.h"
++int plumedswitch;
++plumed plumedmain;
++/* END PLUMED */
++
+ int main(int argc,char *argv[])
+ {
+ const char *desc[] = {
+ #ifdef GMX_OPENMM
+ "This is an experimental release of GROMACS for accelerated",
+@@ -369,11 +375,12 @@
+ { efXVG, "-devout", "deviatie", ffOPTWR },
+ { efXVG, "-runav", "runaver", ffOPTWR },
+ { efXVG, "-px", "pullx", ffOPTWR },
+ { efXVG, "-pf", "pullf", ffOPTWR },
+ { efMTX, "-mtx", "nm", ffOPTWR },
+- { efNDX, "-dn", "dipole", ffOPTWR }
++ { efNDX, "-dn", "dipole", ffOPTWR },
++ { efDAT, "-plumed", "plumed", ffOPTRD } /* PLUMED */
+ };
+ #define NFILE asize(fnm)
+
+ /* Command line options ! */
+ gmx_bool bCart = FALSE;
+@@ -635,16 +642,52 @@
+
+ ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
+ ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
+ ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
+
++/* PLUMED */
++ plumedswitch=0;
++ if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
++ if(plumedswitch){
++ int plumed_is_there=0;
++ int real_precision=sizeof(real);
++ real energyUnits=1.0;
++ real lengthUnits=1.0;
++ real timeUnits=1.0;
++
++ plumed_installed(&plumed_is_there);
++ if(!plumed_is_there){
++ gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
++ }
++ plumedmain=plumed_create();
++ plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
++// this is not necessary for gromacs units:
++ plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
++ plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
++ plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
++//
++ plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
++ plumedswitch=1;
++ }
++/* END PLUMED */
++
++
++
+ rc = mdrunner(nthreads, fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,
+ nstglobalcomm, ddxyz,dd_node_order,rdd,rconstr,
+ dddlb_opt[0],dlb_scale,ddcsx,ddcsy,ddcsz,
+ nstepout,resetstep,nmultisim,repl_ex_nst,repl_ex_seed,
+ pforce, cpt_period,max_hours,deviceOptions,Flags);
+
++/* PLUMED */
++ if(plumedswitch){
++ plumed_finalize(plumedmain);
++ }
++/* END PLUMED */
++
++
++
+ if (gmx_parallel_env_initialized())
+ gmx_finalize();
+
+ if (MULTIMASTER(cr)) {
+ thanx(stderr);
+EOF_EOF
diff --git a/patches/namd-2.7.config b/patches/namd-2.7.config
new file mode 100644
index 000000000..3eff738a2
--- /dev/null
+++ b/patches/namd-2.7.config
@@ -0,0 +1,6 @@
+
+
+function plumed_preliminary_test(){
+# check if the README.txt contains the word NAMD
+ grep -q NAMD README.txt 1>/dev/null 2>/dev/null && test -f */Make.config
+}
diff --git a/patches/namd-2.7.diff b/patches/namd-2.7.diff
new file mode 100644
index 000000000..a11ff41c5
--- /dev/null
+++ b/patches/namd-2.7.diff
@@ -0,0 +1,264 @@
+patch -u -l -b -F 5 --suffix=.preplumed "./Makefile" << \EOF_EOF
+--- ./Makefile.preplumed
++++ ./Makefile
+@@ -347,10 +347,12 @@
+ cat $(BUILDINFO).C; \
+ $(CXX) $(CXXFLAGS) $(COPTO)$(BUILDINFO).o $(COPTC) $(BUILDINFO).C
+
+ all: $(BINARIES) $(LIBCUDARTSO)
+
++include .rootdir/Plumed.inc
++
+ namd2: $(INCDIR) $(DSTDIR) $(OBJS) $(LIBS)
+ $(MAKEBUILDINFO)
+ $(CHARMC) -verbose -ld++-option \
+ "$(COPTI)$(CHARMINC) $(COPTI)$(INCDIR) $(COPTI)$(SRCDIR) $(CXXOPTS)" \
+ -module NeighborLB -module HybridLB -module RefineLB -module GreedyLB -language charm++ \
+@@ -360,10 +362,11 @@
+ $(CUDALIB) \
+ $(DPMTALIB) \
+ $(DPMELIB) \
+ $(TCLLIB) \
+ $(FFTLIB) \
++ $(PLUMED_LOAD) \
+ $(PLUGINLIB) \
+ $(CHARMOPTS) \
+ -lm -o namd2
+
+ charmrun: $(CHARM)/bin/charmrun # XXX
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.C" << \EOF_EOF
+--- ./src/SimParameters.C.preplumed
++++ ./src/SimParameters.C
+@@ -1231,10 +1231,17 @@
+ &colvarsOn, FALSE);
+ opts.require("colvars", "colvarsConfig",
+ "configuration for the collective variables", PARSE_STRING);
+ opts.optional("colvars", "colvarsInput",
+ "input restart file for the collective variables", PARSE_STRING);
++
++ // PLUMED
++ //// plumed
++ opts.optionalB("main", "plumed", "Is PLUMED active?",&plumedOn,FALSE);
++ opts.require("plumed", "plumedfile","PLUMED script",PARSE_STRING);
++ // END PLUMED
++
+ }
+
+
+ /* BEGIN gf */
+ void SimParameters::config_parser_mgridforce(ParseOptions &opts) {
+@@ -3511,11 +3518,11 @@
+ }
+
+ // Global forces configuration
+
+ globalForcesOn = ( tclForcesOn || freeEnergyOn || miscForcesOn ||
+- (IMDon) || SMDOn || TMDOn || colvarsOn );
++ (IMDon) || SMDOn || TMDOn || colvarsOn || plumedOn );
+
+
+ if (tclForcesOn)
+ {
+ iout << iINFO << "TCL GLOBAL FORCES ACTIVE\n";
+@@ -3596,10 +3603,25 @@
+ }
+
+ iout << endi;
+ }
+
++ // PLUMED
++ if (plumedOn)
++ {
++ iout << iINFO << "PLUMED ACTIVE\n";
++
++ current = config->find("plumedfile");
++ iout << iINFO << "PLUMED CONFIG FILE "<< current->data << "\n" << endi;
++ strcpy(plumedFilename,current->data);
++
++ ifstream plumedFile(current->data);
++ if ( ! plumedFile ) NAMD_die("Error reading PLUMED config file.\n");
++
++ }
++ // END PLUMED
++
+ if (IMDon)
+ {
+ iout << iINFO << "INTERACTIVE MD ACTIVE\n";
+ iout << iINFO << "INTERACTIVE MD PORT " << IMDport << "\n";
+ iout << iINFO << "INTERACTIVE MD FREQ " << IMDfreq << "\n";
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/ComputeMgr.C" << \EOF_EOF
+--- ./src/ComputeMgr.C.preplumed
++++ ./src/ComputeMgr.C
+@@ -73,13 +73,134 @@
+ #include "GlobalMasterTcl.h"
+ #include "GlobalMasterSMD.h"
+ #include "GlobalMasterTMD.h"
+ #include "GlobalMasterEasy.h"
+ #include "GlobalMasterMisc.h"
++// PLUMED
++#include "../Plumed.h"
++// END PLUMED
+ #include "GlobalMasterFreeEnergy.h"
+ #include "GlobalMasterColvars.h"
+
++class GlobalMasterPlumed:
++ public GlobalMasterEasy,
++ private PLMD::Plumed
++{
++ std::vector<int> index;
++ std::vector<double> positions;
++ std::vector<double> forces;
++ std::vector<double> masses;
++ std::vector<double> charges;
++ double box[3][3];
++ SimParameters *spar;
++public:
++ GlobalMasterPlumed():
++ GlobalMasterEasy("plumedScript")
++ {
++ easy_init(config);
++ }
++ void easy_init(const char* config)
++ {
++ int realPrecision=sizeof(double);
++ cmd("setRealPrecision",&realPrecision);
++ spar=Node::Object()->simParameters;
++
++ double energyUnits=4.184;
++ double lengthUnits=0.1;
++ double timeUnits=0.001;
++ cmd("setMDEnergyUnits",&energyUnits);
++ cmd("setMDLengthUnits",&lengthUnits);
++ cmd("setMDTimeUnits",&timeUnits);
++
++ cmd("setPlumedDat",spar->plumedFilename);
++
++ int natoms=Node::Object()->molecule->numAtoms;
++ cmd("setNatoms",&natoms);
++
++ cmd("setMDEngine","namd");
++
++ cmd("setLog",stdout);
++
++ double dt=spar->dt;
++ cmd("setTimestep",&dt);
++ cmd("init");
++
++ int s=step+1;
++ cmd("setStep",&s);
++ share();
++
++ }
++
++ void share(){
++ int* p;
++ int n;
++ bool redo=false;
++ cmd("prepareDependencies");
++ cmd("createFullList",&n);
++ cmd("getFullList",&p);
++ if(index.size()!=n)redo=true;
++ if(!redo) for(int i=0;i<n;i++) if(index[i]!=p[i]) { redo=true; break;};
++ if(redo){
++ index.resize(n);
++ modifyRequestedAtoms().resize(0);
++ for(int i=0;i<n;i++){
++ requestAtom(p[i]);
++ index[i]=p[i];
++ };
++ positions.resize(3*n);
++ forces.resize(3*n);
++ charges.resize(n);
++ masses.resize(n);
++ cmd("setAtomsNlocal",&n);
++ cmd("setAtomsGatindex",&index[0]);
++ }
++ cmd("clearFullList");
++ }
++
++ void easy_calc(){
++
++ for(int i=0;i<index.size();i++){
++ Vector coord;
++ getPosition(index[i],coord);
++ positions[3*i+0]=coord.x;
++ positions[3*i+1]=coord.y;
++ positions[3*i+2]=coord.z;
++ masses[i]=Node::Object()->molecule->atommass(i);
++ charges[i]=Node::Object()->molecule->atommass(i);
++ };
++
++ if(spar->lattice.volume()>0.0){
++ for(int i=0;i<3;i++) box[0][i]=spar->lattice.a()[i];
++ for(int i=0;i<3;i++) box[1][i]=spar->lattice.b()[i];
++ for(int i=0;i<3;i++) box[2][i]=spar->lattice.c()[i];
++ cmd("setBox",&box[0][0]);
++ }
++
++ for(int i=0;i<forces.size();i++) forces[i]=0.0;
++
++ cmd("setPositions",&positions[0]);
++ cmd("setForces",&forces[0]);
++
++ cmd("shareData");
++ cmd("performCalc");
++
++ for(int i=0;i<index.size();i++){
++ Vector f;
++ f.x=forces[3*i+0];
++ f.y=forces[3*i+1];
++ f.z=forces[3*i+2];
++ int j=addForce(index[i],f);
++ };
++
++ int s=step+1;
++ cmd("setStep",&s);
++ share();
++
++ }
++};
++
++
+ ComputeMgr::ComputeMgr()
+ {
+ CkpvAccess(BOCclass_group).computeMgr = thisgroup;
+ computeGlobalObject = 0;
+ computeDPMEObject = 0;
+@@ -656,10 +777,16 @@
+ );
+ if (simParams->TMDOn)
+ masterServerObject->addClient(new GlobalMasterTMD());
+ if (simParams->miscForcesOn)
+ masterServerObject->addClient(new GlobalMasterMisc());
++ // PLUMED
++ if (simParams->plumedOn){
++ masterServerObject->addClient(new GlobalMasterPlumed());
++ }
++ // END PLUMED
++
+ if ( simParams->freeEnergyOn )
+ masterServerObject->addClient(new GlobalMasterFreeEnergy());
+ if ( simParams->colvarsOn )
+ masterServerObject->addClient(new GlobalMasterColvars());
+
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./src/SimParameters.h" << \EOF_EOF
+--- ./src/SimParameters.h.preplumed
++++ ./src/SimParameters.h
+@@ -351,10 +351,13 @@
+ char tclBCArgs[128]; // Extra args for calcforces command
+ Bool freeEnergyOn; // Doing free energy perturbation?
+ Bool miscForcesOn; // Using misc forces?
+ Bool colvarsOn; // Using the colvars module?
+
++ Bool plumedOn; // Using Plumed?
++ char plumedFilename[1024]; // Plumed filename
++
+ Bool fixedAtomsOn; // Are there fixed atoms?
+ Bool fixedAtomsForces; // Calculate forces anyway?
+
+ Bool langevinOn; // Flag TRUE-> langevin dynamics active
+ BigReal langevinTemp; // Temperature for Langevin dynamics
+EOF_EOF
diff --git a/patches/patch.sh b/patches/patch.sh
new file mode 100755
index 000000000..e7a2cb0ea
--- /dev/null
+++ b/patches/patch.sh
@@ -0,0 +1,254 @@
+#! /bin/bash
+
+MANUAL="\
++++ PLUMED patch tool HELP +++
+
+Actions (choose only one):
+ -h, --help
+ print this help and exit
+ -p, --patch
+ patch
+ -r, -R, --revert
+ revert
+ -l, --list-engines
+ print a list of available MD engines
+ -s, --save
+ save (FOR DEVELOPERS)
+Options:
+ -e ENGINE, --engine ENGINE
+ set MD engine to ENGINE (default: choose interactively)
+ -m MODE, --mode MODE
+ set link mode to MODE, which can be either static, shared or runtime
+ --static
+ same as --mode static
+ --shared
+ same as --mode shared
+ --runtime
+ same as --mode runtime
+ --root ROOT
+ set path to plumed directory (default: PLUMED_ROOT environment variable)
+ -d FILE, --diff FILE
+ set the path to diff file (default: ROOT/patches/ENGINE.diff) (FOR TESTING)
+ -f, --force
+ force patching (FOR TESTING)
+"
+
+prefix=""
+action=""
+engine=""
+diff=""
+mode=static
+force=""
+
+multiple_actions=
+
+for option
+do
+
+ prefix_option="$prefix$option"
+ prefix=""
+
+ case "$prefix_option" in
+ (--help|-h) echo "$MANUAL" ; exit ;;
+ (--patch|-p) test -n "$action" && multiple_actions=yes ; action=patch ;;
+ (--save|-s) test -n "$action" && multiple_actions=yes ; action=save ;;
+ (--revert|-R|-r) test -n "$action" && multiple_actions=yes ; action=revert ;;
+ (--list-engines|-l) test -n "$action" && multiple_actions=yes ; action=list ;;
+ (--engine=*) engine="${prefix_option#--engine=}" ;;
+ (--mode=*) mode="${prefix_option#--mode=}" ;;
+ (--diff=*) diff="${prefix_option#--diff=}" ;;
+ (--engine|-e) prefix="--engine=" ;;
+ (--root) prefix="--root=" ;;
+ (--diff|-d) prefix="--diff=" ;;
+ (--mode|-m) prefix="--mode=" ;;
+ (--static) mode=static ;;
+ (--shared) mode=shared ;;
+ (--runtime) mode=runtime ;;
+ (--force|-f) force=yes ;;
+ (*)
+ echo "ERROR: Unknown option $prefix_option. Use -h for help."
+ exit
+ esac
+done
+
+if [ -n "$multiple_actions" ] ; then
+ echo "Too many actions. -h for help"
+ exit
+fi
+
+if [ -z "$action" ] ; then
+ echo "Nothing to do. -h for help"
+ exit
+fi
+
+echo "PLUMED patching tool"
+echo
+if [ -z "$PLUMED_ROOT" ]
+then
+ echo "ERROR: I cannot find PLUMED"
+ echo "Please set PLUMED_ROOT environment variable or use --root"
+ exit
+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
+fi
+
+# build MD engines list
+
+mdlist=""
+for file in "$PLUMED_ROOT"/patches/*diff
+do
+ b="${file##*/}"
+ b="${b%.diff}"
+ mdlist="$mdlist $b"
+done
+
+if [ "$action" == list ]
+then
+ echo "Available MD engines:"
+ for file in "$PLUMED_ROOT"/patches/*diff
+ do
+ b="${file##*/}"
+ b="${b%.diff}"
+ echo " $b"
+ done
+ exit
+fi
+
+if [ -z "$engine" ]
+then
+ PS3="Choose the best matching code/version:"
+ select engine in $mdlist; do
+ if [[ -n "$engine" ]] ; then
+ break
+ else
+ echo "ERROR: choose in the list above or interrupt (^c)"
+ fi
+ done
+fi
+
+if [ -z "$diff" ]
+then
+ diff="$PLUMED_ROOT/patches/${engine}.diff"
+fi
+if [ -z "$config" ]
+then
+ config="$PLUMED_ROOT/patches/${engine}.config"
+fi
+
+echo "MD engine: $engine"
+echo "PLUMED location: $PLUMED_ROOT"
+echo "diff file: $diff"
+
+if [ -f "$config" ]
+then
+ echo "sourcing config file: $config"
+ source "$config"
+fi
+
+case "$mode" in
+(static|shared|runtime) ;;
+(*)
+ echo "I don't understand mode $mode"
+ exit
+esac
+
+
+case "$action" in
+ (patch)
+ if [ ! -f "$diff" ] ; then
+ echo "ERROR: MD engine not supported (or mispelled)"
+ exit
+ fi
+ if type -t plumed_preliminary_test 1>/dev/null ; then
+ if plumed_preliminary_test || [ "$force" ] ; then
+ echo >/dev/null
+ else
+ 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
+ fi
+ fi
+ if [ -L Plumed.h -o -L Plumed.inc ]
+ then
+ echo "ERROR: you have likely already patched. Revert first (-r)"
+ exit
+ fi
+ if [ ! -f "$PLUMED_ROOT/src/Plumed.inc" ]
+ then
+ echo "ERROR: cannot find $PLUMED_ROOT/src/Plumed.inc file"
+ echo "Compile plumed before patching"
+ exit
+ fi
+ echo "Linking Plumed.h and Plumed.inc ($mode mode)"
+ ln -s "$PLUMED_ROOT/src/Plumed.h"
+ ln -s "$PLUMED_ROOT/src/Plumed.inc.$mode" Plumed.inc
+ bash "$diff"
+ ;;
+ (save)
+ 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
+ fi
+ PREPLUMED=$(find . -name "*.preplumed")
+ if ! test "$PREPLUMED" ; then
+ echo "ERROR: I cannot find any .preplumed file. You have likely not patched yet."
+ exit
+ fi
+ if type -t plumed_preliminary_test 1>/dev/null ; then
+ if plumed_preliminary_test || [ "$force" ] ; then
+ echo >/dev/null
+ else
+ 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
+ fi
+ fi
+ echo "Saving your changes to $diff"
+ echo "Preplumed files:"
+ echo "$PREPLUMED"
+ test -e "$diff" && rm "$diff"
+ for bckfile in $PREPLUMED ; do
+ file="${bckfile%.preplumed}"
+ if test -e "$file" ; then
+ echo "patch -u -l -b -F 5 --suffix=.preplumed \"${file}\" << \\EOF_EOF" >> "$diff"
+ diff -U 5 "${bckfile}" "$file" --label="$bckfile" --label="$file" >> "$diff"
+ echo "EOF_EOF" >> "$diff"
+ else
+ echo "ERROR: File $file is missing"
+ fi
+ done
+ ;;
+ (revert)
+ if [ ! -f "$diff" ] ; then
+ echo "ERROR: MD engine not supported (or mispelled)"
+ exit
+ fi
+ if [ ! -L Plumed.h -o ! -L Plumed.inc ]
+ then
+ echo "WARNING: I cannot find Plumed.h and Plumed.inc files. You have likely not patched yet."
+ else
+ echo "Removing Plumed.h and Plumed.inc"
+ rm Plumed.h Plumed.inc
+ fi
+ PREPLUMED=$(find . -name "*.preplumed")
+ if ! test "$PREPLUMED" ; then
+ echo "WARNING: I cannot find any .preplumed file. You have likely not patched yet."
+ else
+ echo "Reverting changes and touching reverted files"
+ for bckfile in $PREPLUMED ; do
+ file="${bckfile%.preplumed}"
+ mv "$bckfile" "$file"
+ touch "$file"
+ done
+ fi
+esac
+
+
+
diff --git a/src/.gitignore b/src/.gitignore
new file mode 100644
index 000000000..294976305
--- /dev/null
+++ b/src/.gitignore
@@ -0,0 +1,2 @@
+Plumed.inc*
+PlumedConfig.h
diff --git a/src/Action.cpp b/src/Action.cpp
new file mode 100644
index 000000000..5021afe7e
--- /dev/null
+++ b/src/Action.cpp
@@ -0,0 +1,83 @@
+#include "Action.h"
+#include "PlumedMain.h"
+#include "Log.h"
+#include <cassert>
+
+using namespace PLMD;
+
+ActionOptions::ActionOptions(PlumedMain&p,const std::vector<std::string>&l):
+plumed(p),
+line(l)
+{
+}
+
+Action::Action(const ActionOptions&ao):
+ name(ao.line[0]),
+ line(ao.line),
+ active(false),
+ plumed(ao.plumed),
+ log(plumed.getLog()),
+ comm(plumed.comm)
+{
+ line.erase(line.begin());
+ log.printf("Action %s\n",name.c_str());
+ parse("LABEL",label);
+ if(label.length()==0){
+ std::string s; Tools::convert(plumed.getActionSet().size(),s);
+ label="@"+s;
+ }
+ log.printf(" with label %s\n",label.c_str());
+}
+
+void Action::parseFlag(const std::string&key,bool & t){
+ if(!Tools::parseFlag(line,key,t)){
+ log.printf("ERROR parsing keyword %s\n",key.c_str());
+ log.printf("%s\n",getDocumentation().c_str());
+ this->exit(1);
+ }
+}
+
+void Action::addDependency(Action*action){
+ assert(this->after.count(action)==action->before.count(this));
+ this->after.insert(action);
+ action->before.insert(this);
+}
+
+void Action::activate(){
+ active=true;
+ for(Dependencies::iterator p=after.begin();p!=after.end();p++) (*p)->activate();
+}
+
+void Action::clearDependencies(){
+ for(Dependencies::iterator p=after.begin();p!=after.end();p++){
+ (*p)->before.erase(this);
+ };
+ this->after.clear();
+}
+
+std::string Action::getDocumentation()const{
+ return std::string("UNDOCUMENTED ACTION");
+}
+
+void Action::checkRead(){
+ if(line.size()>0){
+ log.printf("ERROR READING INPUT FILE\n%s\n",getDocumentation().c_str());
+ exit(1);
+ }
+}
+
+int Action::getStep()const{
+ return plumed.getStep();
+}
+
+double Action::getTime()const{
+ return plumed.getAtoms().getTimeStep()*getStep();
+}
+
+
+
+void Action::exit(int c){
+ plumed.exit(c);
+}
+
+
diff --git a/src/Action.h b/src/Action.h
new file mode 100644
index 000000000..b1f23d4bb
--- /dev/null
+++ b/src/Action.h
@@ -0,0 +1,166 @@
+#ifndef __PLUMED_Action_h
+#define __PLUMED_Action_h
+#include <vector>
+#include <string>
+#include <set>
+#include "Log.h"
+#include "Tools.h"
+
+#include "PlumedCommunicator.h"
+
+namespace PLMD{
+
+class PlumedMain;
+
+/// This class is used to bring the relevant information to the Action constructor.
+/// Its content is kept private to other classes, and may change in the future
+class ActionOptions{
+ friend class Action;
+ friend class ActionRegister;
+/// Reference to main PlumedMain object
+ PlumedMain& plumed;
+/// Input line which sets up the action
+ std::vector<std::string> line;
+public:
+/// Constructor
+ ActionOptions(PlumedMain&p,const std::vector<std::string>&);
+};
+
+/// Base class for all the input Actions.
+/// The input Actions are more or less corresponding to the directives
+/// in the plumed.dat file and are applied in order at each time-step.
+class Action
+{
+
+/// Name of the directive in the plumed.dat file.
+ const std::string name;
+
+/// Label of the Action, as set with LABEL= in the plumed.dat file.
+ std::string label;
+
+/// Directive line.
+/// This line is progressively erased during Action construction
+/// so as to check if all the present keywords are correct.
+ std::vector<std::string> line;
+
+ typedef std::set<Action*> Dependencies;
+/// Actions on which this Action depends.
+ Dependencies after;
+/// Actions depending on this Action.
+ Dependencies before;
+
+/// Switch to activate Action on this step.
+ bool active;
+
+protected:
+
+/// Reference to main plumed object
+ PlumedMain& plumed;
+
+/// Reference to the log stream
+ Log& log;
+
+/// Specify that this Action depends on another one
+ void addDependency(Action*);
+
+/// Clear the dependence list for this Action
+ void clearDependencies();
+
+/// Return the present timestep
+ int getStep()const;
+
+/// Return the present time
+ double getTime()const;
+
+/// Check if Action was properly read.
+/// This checks if Action::line is empty. It must be called after
+/// a final Action has been initialized
+ void checkRead();
+
+/// Parse one keyword as generic type
+ template<class T>
+ void parse(const std::string&key,T&t);
+
+/// Parse one keyword as std::vector
+ template<class T>
+ void parseVector(const std::string&key,std::vector<T>&t);
+
+/// Parse one keyword as boolean flag
+ void parseFlag(const std::string&key,bool&t);
+
+/// Exit with error code c
+ void exit(int c=0);
+
+public:
+ Action(const ActionOptions&);
+ virtual ~Action(){};
+
+ PlumedCommunicator& comm;
+
+/// Calculate an Action.
+/// This method is called one or more times per step.
+/// The set of all Actions is calculated in forward order.
+ virtual void calculate()=0;
+
+/// Apply an Action.
+/// This method is called one time per step.
+/// The set of all Actions is applied in backword order.
+ virtual void apply()=0;
+
+/// Tell to the Action to flush open files
+ virtual void flush(){};
+
+ virtual std::string getDocumentation()const;
+
+/// Returns the label
+ const std::string & getLabel()const;
+
+/// Set action to active
+ virtual void activate();
+
+/// Set action to inactive
+ virtual void deactivate();
+
+/// Check if action is active
+ bool isActive()const;
+};
+
+/////////////////////
+// FAST INLINE METHODS
+
+inline
+const std::string & Action::getLabel()const{
+ return label;
+}
+
+template<class T>
+void Action::parse(const std::string&key,T&t){
+ if(!Tools::parse(line,key,t)){
+ log.printf("ERROR parsing keyword %s\n",key.c_str());
+ log.printf("%s\n",getDocumentation().c_str());
+ this->exit(1);
+ }
+}
+
+template<class T>
+void Action::parseVector(const std::string&key,std::vector<T>&t){
+ if(!Tools::parseVector(line,key,t)){
+ log.printf("ERROR parsing keyword %s\n",key.c_str());
+ log.printf("%s\n",getDocumentation().c_str());
+ this->exit(1);
+ }
+}
+
+inline
+void Action::deactivate(){
+ active=false;
+}
+
+inline
+bool Action::isActive()const{
+ return active;
+}
+
+}
+#endif
+
diff --git a/src/ActionAtomistic.cpp b/src/ActionAtomistic.cpp
new file mode 100644
index 000000000..44500a6f1
--- /dev/null
+++ b/src/ActionAtomistic.cpp
@@ -0,0 +1,49 @@
+#include "ActionAtomistic.h"
+#include "PlumedMain.h"
+#include <vector>
+#include <string>
+#include <cassert>
+
+using namespace std;
+using namespace PLMD;
+
+ActionAtomistic::~ActionAtomistic(){
+// forget the pending request
+ if(atomRequest) delete atomRequest;
+}
+
+ActionAtomistic::ActionAtomistic(const ActionOptions&ao):
+Action(ao),
+atomRequest(NULL)
+{
+ parse("SIGMA",sigma);
+ log.printf(" with sigma %f\n",sigma);
+}
+
+void ActionAtomistic::activate(){
+ if(atomRequest) atomRequest->activate();
+ Action::activate();
+}
+
+void ActionAtomistic::deactivate(){
+ if(atomRequest) atomRequest->deactivate();
+ Action::deactivate();
+}
+
+void ActionAtomistic::requestAtoms(const vector<int> & a){
+ int nat=a.size();
+ indexes=a;
+ positions.resize(nat);
+ forces.resize(nat);
+ masses.resize(nat);
+ charges.resize(nat);
+ if(atomRequest) delete atomRequest;
+// atomRequest=new Atoms::Request(plumed.getAtoms(),indexes,positions,forces,box,virial);
+ atomRequest=new Atoms::Request(plumed.getAtoms(),indexes,masses,charges,positions,forces,box,virial);
+}
+
+Vector ActionAtomistic::pbcDistance(const Vector &v1,const Vector &v2)const{
+ return plumed.getAtoms().getPbc().distance(v1,v2);
+}
+
+
diff --git a/src/ActionAtomistic.h b/src/ActionAtomistic.h
new file mode 100644
index 000000000..0b561e325
--- /dev/null
+++ b/src/ActionAtomistic.h
@@ -0,0 +1,101 @@
+#ifndef __PLUMED_ActionAtomistic_h
+#define __PLUMED_ActionAtomistic_h
+
+#include <vector>
+#include <string>
+#include "Action.h"
+#include "Atoms.h"
+
+namespace PLMD {
+
+/// Action which can access to atomistic data
+class ActionAtomistic :
+ virtual public Action
+ {
+
+ double sigma; // typical variable scale
+ Atoms::Request* atomRequest; // handler for request of atoms
+ std::vector<int> indexes; // the set of needed atoms
+ std::vector<Vector> positions; // positions of the needed atoms
+ Tensor box;
+ Tensor virial;
+ std::vector<Vector> forces; // forces on the needed atoms
+ std::vector<double> masses;
+ std::vector<double> charges;
+
+protected:
+ void requestAtoms(const std::vector<int> & a);
+ const Vector & getPositions(int)const;
+ const Tensor & getBox()const;
+ const std::vector<Vector> & getPositions()const;
+ double getMasses(int i)const;
+ double getCharges(int i)const;
+ std::vector<Vector> & modifyForces();
+ Tensor & modifyVirial();
+ int getNatoms(){return indexes.size();};
+ Vector pbcDistance(const Vector&,const Vector&)const;
+
+public:
+
+// virtual functions:
+
+ ActionAtomistic(const ActionOptions&ao);
+ ~ActionAtomistic();
+
+ void activate();
+ void deactivate();
+
+ void clearOutputForces();
+};
+
+inline
+const Vector & ActionAtomistic::getPositions(int i)const{
+ return positions[i];
+}
+
+inline
+double ActionAtomistic::getMasses(int i)const{
+ return masses[i];
+}
+
+inline
+double ActionAtomistic::getCharges(int i)const{
+ return charges[i];
+}
+
+
+inline
+const std::vector<Vector> & ActionAtomistic::getPositions()const{
+ return positions;
+}
+
+
+inline
+const Tensor & ActionAtomistic::getBox()const{
+ return box;
+}
+
+inline
+std::vector<Vector> & ActionAtomistic::modifyForces(){
+ return forces;
+}
+
+inline
+Tensor & ActionAtomistic::modifyVirial(){
+ return virial;
+}
+
+inline
+void ActionAtomistic::clearOutputForces(){
+ for(unsigned i=0;i<forces.size();++i){
+ forces[i][0]=0.0;
+ forces[i][1]=0.0;
+ forces[i][2]=0.0;
+ }
+}
+
+
+
+}
+
+#endif
diff --git a/src/ActionPilot.cpp b/src/ActionPilot.cpp
new file mode 100644
index 000000000..63790a44c
--- /dev/null
+++ b/src/ActionPilot.cpp
@@ -0,0 +1,24 @@
+#include "ActionPilot.h"
+#include "PlumedMain.h"
+#include <cassert>
+
+using namespace PLMD;
+using namespace std;
+
+ActionPilot::ActionPilot(const ActionOptions&ao):
+Action(ao),
+stride(1)
+{
+ parse("STRIDE",stride);
+ log.printf(" with stride %d\n",stride);
+}
+
+bool ActionPilot::onStep()const{
+ return getStep()%stride==0;
+}
+
+int ActionPilot::getStride()const{
+ return stride;
+}
+
+
diff --git a/src/ActionPilot.h b/src/ActionPilot.h
new file mode 100644
index 000000000..a0e69cc75
--- /dev/null
+++ b/src/ActionPilot.h
@@ -0,0 +1,25 @@
+#ifndef __PLUMED_ActionPilot_h
+#define __PLUMED_ActionPilot_h
+
+#include "Action.h"
+
+namespace PLMD{
+
+/// Action which drives the execution of other Action's.
+/// Action's of this kind are executed with a fixed stride
+/// which is specified on the directive line with a STRIDE= keyword
+class ActionPilot:
+ public virtual Action
+{
+ int stride; // multiple time step
+protected:
+ int getStride()const;
+public:
+ ActionPilot(const ActionOptions&);
+ bool onStep()const;
+};
+
+}
+
+#endif
+
diff --git a/src/ActionRegister.cpp b/src/ActionRegister.cpp
new file mode 100644
index 000000000..48e16a75b
--- /dev/null
+++ b/src/ActionRegister.cpp
@@ -0,0 +1,59 @@
+#include "ActionRegister.h"
+#include "Log.h"
+#include "Tools.h"
+#include <algorithm>
+#include <cassert>
+
+
+using namespace std;
+using namespace PLMD;
+
+ActionRegister& PLMD::actionRegister(){
+ static ActionRegister* ans = new ActionRegister;
+ return *ans;
+}
+
+void ActionRegister::add(string key,creator_pointer f){
+ if(m.count(key)){
+ m.erase(key);
+ disabled.insert(key);
+ }else{
+ m.insert(pair<string,creator_pointer>(key,f));
+ };
+}
+
+bool ActionRegister::check(string key){
+ if(m.count(key)>0) return true;
+ return false;
+}
+
+Action* ActionRegister::create(const ActionOptions&ao){
+ if(ao.line.size()<1)return NULL;
+ Action* action;
+ if(m[ao.line[0]]) action=m[ao.line[0]](ao);
+ else action=NULL;
+ return action;
+}
+
+void ActionRegister::log(Log & log){
+ vector<string> s;
+ for(mIterator it=m.begin();it!=m.end();++it)
+ s.push_back((*it).first);
+ sort(s.begin(),s.end());
+ for(unsigned i=0;i<s.size();i++){
+ log.printf(" %s\n",s[i].c_str());
+ };
+ if(disabled.size()>0){
+ s.assign(disabled.size(),"");
+ copy(disabled.begin(),disabled.end(),s.begin());
+ sort(s.begin(),s.end());
+ log.printf("+++++++ WARNING +++++++\n");
+ log.printf("The following keywords have been registered more than once and will be disabled:\n");
+ for(unsigned i=0;i<s.size();i++){
+ log.printf(" - %s\n",s[i].c_str());
+ };
+ log.printf("+++++++ END WARNING +++++++\n");
+ };
+}
+
+
diff --git a/src/ActionRegister.h b/src/ActionRegister.h
new file mode 100644
index 000000000..795c760f7
--- /dev/null
+++ b/src/ActionRegister.h
@@ -0,0 +1,69 @@
+#ifndef __PLUMED_ActionRegister_h
+#define __PLUMED_ActionRegister_h
+
+#include <map>
+#include <set>
+#include "Action.h"
+
+namespace PLMD{
+
+class Log;
+
+/// Register holding all the allowed keywords.
+/// This is a register which holds a map between strings (directives) and function pointers.
+/// The function pointers are pointing to functions which create an object of
+/// the corresponding class given the corresponding options (ActionOptions).
+/// There should be only one of there objects allocated.
+/// Actions should be registered here at the beginning of execution
+/// If the same directive is used for different classes, it is automatically disabled
+/// to avoid random results.
+///
+class ActionRegister{
+/// Pointer to a function which, given the options, create an Action
+ typedef Action*(*creator_pointer)(const ActionOptions&);
+/// Map action to a function which creates the related object
+ std::map<std::string,creator_pointer> m;
+/// Iterator over the map
+ typedef std::map<std::string,creator_pointer>::iterator mIterator;
+/// Set of disabled actions (which were registered more than once)
+ std::set<std::string> disabled;
+public:
+/// Register a new class.
+/// \param key The name of the directive to be used in the input file
+/// \param key A pointer to a function which creates an object of that class
+ void add(std::string key,creator_pointer);
+/// Verify if a directive is present in the register
+ bool check(std::string action);
+/// Create an Action of the type indicated in the options
+/// \param ao object containing information for initialization, such as the full input line, a pointer to PlumedMain, etc
+ Action* create(const ActionOptions&ao);
+/// Write on the log stream the list of registered directives
+ void log(Log & log);
+};
+
+/// Function returning a reference to the ActionRegister.
+/// \relates ActionRegister
+/// To avoid problems with order of initialization, this function contains
+/// a static ActionRegister which is built the first time the function is called.
+/// In this manner, it is always initialized before it's used
+ActionRegister& actionRegister();
+
+}
+
+
+/// Shortcut for Action registration
+/// \relates PLMD::ActionRegister
+/// For easier registration, this file also provides a macro PLUMED_REGISTER_ACTION.
+/// \param classname the name of the class to be registered
+/// \param directive a string containing the corresponding directive
+/// This macro should be used in the .cpp file of the corresponding class
+#define PLUMED_REGISTER_ACTION(classname,directive) \
+ static class classname##RegisterMe{ \
+ static PLMD::Action* create(const PLMD::ActionOptions&ao){return new classname(ao);} \
+ public: \
+ classname##RegisterMe(){PLMD::actionRegister().add(directive,create);}; \
+ } classname##RegisterMeObject;
+
+
+#endif
+
diff --git a/src/ActionSet.cpp b/src/ActionSet.cpp
new file mode 100644
index 000000000..fa09fecd7
--- /dev/null
+++ b/src/ActionSet.cpp
@@ -0,0 +1,15 @@
+#include "ActionSet.h"
+#include "PlumedMain.h"
+
+using namespace std;
+using namespace PLMD;
+
+ActionSet::ActionSet(PlumedMain&p):
+plumed(p){
+}
+
+void ActionSet::clearDelete(){
+ for(int i=size()-1;i>=0;i--) delete (*this)[i];
+ clear();
+}
+
diff --git a/src/ActionSet.h b/src/ActionSet.h
new file mode 100644
index 000000000..faf112381
--- /dev/null
+++ b/src/ActionSet.h
@@ -0,0 +1,79 @@
+#ifndef __PLUMED_ActionSet_h
+#define __PLUMED_ActionSet_h
+
+#include "Action.h"
+
+namespace PLMD {
+
+class PlumedMain;
+
+/// std::vector containing the sequence of Action to be done.
+/// It is a vector of Action*, and as such it has the entire
+/// std::vector interface. Moreover, it implements methods to extract
+/// Acion* of a given type (select<T>()), NOT of a given type (selectNot<T>())
+/// or to find an Action with a given label (selectWithLabel())
+/// Finally, since it holds pointers, there is a clearDelete() function
+/// which deletes the pointers before deleting the vector
+class ActionSet:
+ public std::vector<Action*>
+{
+ PlumedMain& plumed;
+public:
+ ActionSet(PlumedMain&p);
+/// Clear and deletes all the included pointers.
+ void clearDelete();
+
+/// Extract pointers to all Action's of type T
+/// To extract all Colvar , use select<Colvar*>();
+ template <class T>
+ std::vector<T> select()const;
+/// Extract pointers to all Action's which are not of type T
+/// E.g., to extract all noncolvars, use
+/// selectNot<Colvar*>();
+ template <class T>
+ std::vector<Action*> selectNot()const;
+/// Extract pointer to an action labeled s, only if it is of
+/// type T. E.g., to extract an action labeled "pippo", use selectWithLabel<Action*>("pippo")
+/// If you want it to be a Colvar, use selectWithLabel<Colvar*>(pippo). If it is
+/// not found, it returns NULL
+ template <class T>
+ T selectWithLabel(const std::string&s)const;
+};
+
+///////
+// INLINE IMPLEMENTATIONS:
+
+template <class T>
+std::vector<T> ActionSet::select()const{
+ std::vector<T> ret;
+ for(const_iterator p=begin();p!=end();++p){
+ T t=dynamic_cast<T>(*p);
+ if(t) ret.push_back(t);
+ };
+ return ret;
+}
+
+template <class T>
+T ActionSet::selectWithLabel(const std::string&s)const{
+ std::vector<T> ret;
+ for(const_iterator p=begin();p!=end();++p){
+ T t=dynamic_cast<T>(*p);
+ if(t && dynamic_cast<Action*>(t)->getLabel()==s) return t;
+ };
+ return NULL;
+}
+
+template <class T>
+std::vector<Action*> ActionSet::selectNot()const{
+ std::vector<Action*> ret;
+ for(const_iterator p=begin();p!=end();++p){
+ T t=dynamic_cast<T>(*p);
+ if(!t) ret.push_back(*p);
+ };
+ return ret;
+}
+
+}
+
+#endif
+
diff --git a/src/ActionSetup.cpp b/src/ActionSetup.cpp
new file mode 100644
index 000000000..d973ac4d3
--- /dev/null
+++ b/src/ActionSetup.cpp
@@ -0,0 +1,15 @@
+#include "ActionSetup.h"
+#include "PlumedMain.h"
+
+using namespace PLMD;
+
+ActionSetup::ActionSetup(const ActionOptions&ao):
+ Action(ao)
+{
+ const ActionSet& actionset(plumed.getActionSet());
+ for(ActionSet::const_iterator p=actionset.begin();p!=actionset.end();++p){
+// check that all the preceeding actions are ActionSetup
+ assert(dynamic_cast<ActionSetup*>(*p));
+ }
+}
+
diff --git a/src/ActionSetup.h b/src/ActionSetup.h
new file mode 100644
index 000000000..88a308190
--- /dev/null
+++ b/src/ActionSetup.h
@@ -0,0 +1,23 @@
+#ifndef __PLUMED_ActionSetup_h
+#define __PLUMED_ActionSetup_h
+
+#include "Action.h"
+
+
+namespace PLMD{
+
+/// Action executed only at startup
+class ActionSetup :
+ public virtual Action {
+public:
+/// Constructor
+ ActionSetup(const ActionOptions&ao);
+/// Do nothing.
+ void calculate(){};
+/// Do nothing.
+ void apply(){};
+};
+
+}
+
+#endif
diff --git a/src/ActionWithArguments.cpp b/src/ActionWithArguments.cpp
new file mode 100644
index 000000000..3440f3495
--- /dev/null
+++ b/src/ActionWithArguments.cpp
@@ -0,0 +1,65 @@
+#include "ActionWithArguments.h"
+#include "PlumedMain.h"
+
+using namespace std;
+using namespace PLMD;
+
+ActionWithArguments::ActionWithArguments(const ActionOptions&ao):
+ Action(ao)
+{
+ string args;
+ parse("ARG",args);
+
+ vector<string> c=Tools::getWords(args,",");
+
+ for(unsigned i=0;i<c.size();i++){
+ std::size_t dot=c[i].find_first_of('.');
+ if(dot!=string::npos){
+ string a=c[i].substr(0,dot);
+ string name=c[i].substr(dot+1);
+ if(a=="*"){
+ assert(name=="*");
+ std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
+ for(unsigned j=0;j<all.size();j++){
+ for(int k=0;k<all[j]->getNumberOfValues();++k){
+ arguments.push_back(all[j]->getValue(k));
+ }
+ };
+ } else {
+ ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
+ assert(action);
+ if(name=="*"){
+ vector<string> s=action->getValueNames();
+ for(unsigned j=0;j<s.size();j++)arguments.push_back(action->getValue(s[j]));
+ } else {
+ assert(action->hasNamedValue(name));
+ arguments.push_back(action->getValue(name));
+ }
+ }
+ } else if(c[i]=="*"){
+ std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
+ for(unsigned j=0;j<all.size();j++){
+ assert(all[j]->hasNamedValue(""));
+ arguments.push_back(all[j]->getValue(""));
+ };
+ } else{
+ ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(c[i]);
+ assert(action);
+ assert(action->hasNamedValue(""));
+ arguments.push_back(action->getValue(""));
+ }
+ }
+
+ if(c.size()>0){
+ log.printf(" with arguments");
+ for(unsigned i=0;i<c.size();i++) log.printf(" %s",c[i].c_str());
+ log.printf("\n");
+ }
+
+ clearDependencies();
+ for(unsigned i=0;i<arguments.size();i++) addDependency(&arguments[i]->getAction());
+}
+
+
+
+
diff --git a/src/ActionWithArguments.h b/src/ActionWithArguments.h
new file mode 100644
index 000000000..c344601bb
--- /dev/null
+++ b/src/ActionWithArguments.h
@@ -0,0 +1,49 @@
+#ifndef __PLUMED_ActionWithArguments_h
+#define __PLUMED_ActionWithArguments_h
+
+#include "Action.h"
+#include <map>
+#include <vector>
+#include <cassert>
+
+#include "ActionWithValue.h"
+
+namespace PLMD{
+
+/// Action which takes other Action's as arguments.
+/// Arguments are objects of type PLMD::Value, and
+/// are addressed using the ARG= keyword on the directive line
+class ActionWithArguments:
+ public virtual Action
+{
+ std::vector<Value*> arguments;
+
+protected:
+ ActionWithArguments(const ActionOptions&);
+ virtual ~ActionWithArguments(){};
+ std::vector<Value*> & getArguments();
+ double getArgument(int)const;
+ unsigned getNumberOfArguments()const;
+public:
+};
+
+
+inline
+std::vector<Value*> & ActionWithArguments::getArguments(){
+ return arguments;
+}
+
+inline
+double ActionWithArguments::getArgument(int i)const{
+ return arguments[i]->getValue();
+}
+
+inline
+unsigned ActionWithArguments::getNumberOfArguments()const{
+ return arguments.size();
+}
+
+
+}
+
+#endif
diff --git a/src/ActionWithValue.cpp b/src/ActionWithValue.cpp
new file mode 100644
index 000000000..6a93d3ba7
--- /dev/null
+++ b/src/ActionWithValue.cpp
@@ -0,0 +1,69 @@
+#include "ActionWithValue.h"
+#include "PlumedMain.h"
+
+using namespace std;
+using namespace PLMD;
+
+
+
+ActionWithValue::ActionWithValue(const ActionOptions&ao):
+ Action(ao),
+ numberOfParameters(0)
+{}
+
+ActionWithValue::~ActionWithValue(){
+ for(unsigned i=0;i<values.size();++i)delete values[i];
+}
+
+void ActionWithValue::addValue(const std::string&name){
+ assertUnique(name);
+ values.push_back(new Value(*this,name));
+}
+
+void ActionWithValue::addValueWithDerivatives(const std::string&name){
+ assertUnique(name);
+ Value* v=new Value(*this,name);
+ v->enableDerivatives();
+ values.push_back(v);
+}
+
+bool ActionWithValue::hasNamedValue(const std::string&name)const{
+ for(unsigned i=0;i<values.size();++i){
+ if(name==values[i]->getName()) return true;
+ }
+ return false;
+}
+
+int ActionWithValue::getValueIndex(const std::string&name)const{
+ for(unsigned i=0;i<values.size();++i) if(name==values[i]->getName()) return i;
+ assert(0);
+ return -1; // otherwise the compiler complains
+}
+
+Value* ActionWithValue::getValue(const std::string&name)const{
+ return values[getValueIndex(name)];
+}
+
+Value* ActionWithValue::getValue(int i)const{
+ return values[i];
+}
+
+std::vector<std::string> ActionWithValue::getValueNames()const{
+ std::vector<std::string> ret;
+ for(unsigned i=0;i<values.size();i++) ret.push_back(values[i]->getName());
+ return ret;
+}
+
+void ActionWithValue::setNumberOfParameters(int n){
+ numberOfParameters=n;
+ for(unsigned i=0;i<values.size();i++) values[i]->setNumberOfParameters(n);
+}
+
+void ActionWithValue::clearInputForces(){
+ for(unsigned i=0;i<values.size();i++) values[i]->clearInputForce();
+}
+void ActionWithValue::clearDerivatives(){
+ for(unsigned i=0;i<values.size();i++) values[i]->clearDerivatives();
+}
+
+
diff --git a/src/ActionWithValue.h b/src/ActionWithValue.h
new file mode 100644
index 000000000..4b4dcd654
--- /dev/null
+++ b/src/ActionWithValue.h
@@ -0,0 +1,74 @@
+#ifndef __PLUMED_ActionWithValue_h
+#define __PLUMED_ActionWithValue_h
+
+#include "Action.h"
+#include <map>
+#include <vector>
+#include <cassert>
+#include "Value.h"
+
+namespace PLMD{
+
+/// Action which can take one or more values.
+/// This object contains an array of PLMD::Value, one for each component.
+class ActionWithValue:
+ public virtual Action
+{
+ int numberOfParameters;
+ std::vector<Value*> values;
+ void assertUnique(const std::string&name);
+ int getValueIndex(const std::string&name)const;
+public:
+ ActionWithValue(const ActionOptions&ao);
+ ~ActionWithValue();
+ void addValue(const std::string&name);
+ void addValueWithDerivatives(const std::string&name);
+ bool hasNamedValue(const std::string&name)const;
+ Value* getValue(const std::string&name)const;
+ Value* getValue(int i)const;
+ std::vector<std::string> getValueNames()const;
+ int getNumberOfValues();
+ void setNumberOfParameters(int n);
+ int getNumberOfParameters()const;
+ double getForce(int n);
+ void addInputForces(int i,double f);
+ void clearInputForces();
+ void clearDerivatives();
+ void setValue(Value*,double);
+ void setValue(double);
+};
+
+inline
+void ActionWithValue::setValue(Value*v,double d){
+ v->setValue(d);
+}
+
+inline
+void ActionWithValue::setValue(double d){
+ values[0]->setValue(d);
+}
+
+inline
+void ActionWithValue::addInputForces(int i,double f){values[i]->addForce(f);}
+
+inline
+double ActionWithValue::getForce(int n){return values[n]->getForce();}
+
+inline
+void ActionWithValue::assertUnique(const std::string&name){
+ assert(!hasNamedValue(name));
+}
+
+inline
+int ActionWithValue::getNumberOfValues(){return values.size();}
+
+inline
+int ActionWithValue::getNumberOfParameters()const{
+ return numberOfParameters;
+}
+
+
+
+}
+
+#endif
diff --git a/src/Atoms.cpp b/src/Atoms.cpp
new file mode 100644
index 000000000..663906379
--- /dev/null
+++ b/src/Atoms.cpp
@@ -0,0 +1,297 @@
+#include "Atoms.h"
+#include <cassert>
+#include <algorithm>
+#include <string>
+
+#include "MDAtoms.h"
+#include "PlumedMain.h"
+
+using namespace PLMD;
+using namespace std;
+
+namespace PLMD {
+
+class PlumedMain;
+
+Atoms::Atoms(PlumedMain&plumed):
+ natoms(0),
+ energy(0.0),
+ collectEnergy(0.0),
+ plumed(plumed),
+ MDEnergyUnits(1.0),
+ MDLengthUnits(1.0),
+ MDTimeUnits(1.0),
+ internalEnergyUnits(1.0),
+ internalLengthUnits(1.0),
+ internalTimeUnits(1.0),
+ forceOnEnergy(0.0)
+{
+ mdatoms=MDAtomsBase::create(sizeof(double));
+}
+
+Atoms::~Atoms(){
+ if(mdatoms) delete mdatoms;
+}
+
+void Atoms::setBox(void*p){
+ mdatoms->setBox(p);
+ Tensor b; mdatoms->getBox(b);
+ pbc.setBox(b);
+}
+
+void Atoms::setPositions(void*p){
+ mdatoms->setp(p);
+}
+
+void Atoms::setMasses(void*p){
+ mdatoms->setm(p);
+}
+
+void Atoms::setCharges(void*p){
+ mdatoms->setc(p);
+}
+
+void Atoms::setVirial(void*p){
+ mdatoms->setVirial(p);
+}
+
+void Atoms::setEnergy(void*p){
+ MD2double(p,energy);
+ energy*=MDEnergyUnits/internalEnergyUnits;
+}
+
+void Atoms::setForces(void*p){
+ mdatoms->setf(p);
+}
+
+void Atoms::setPositions(void*p,int i){
+ mdatoms->setp(p,i);
+}
+
+void Atoms::setForces(void*p,int i){
+ mdatoms->setf(p,i);
+}
+
+void Atoms::share(){
+ mdatoms->getBox(box);
+ mdatoms->getMasses(gatindex,masses);
+ mdatoms->getCharges(gatindex,charges);
+ mdatoms->getPositions(gatindex,positions);
+ if(dd && gatindex.size()<natoms){
+ std::set<int> unique;
+ for(unsigned i=0;i<requestset.size();i++){
+ if(requestset[i]->isActive()) unique.insert(requestset[i]->unique.begin(),requestset[i]->unique.end());
+ }
+ for(unsigned i=0;i<dd.mpi_request_positions.size();i++) dd.mpi_request_positions[i].wait();
+ for(unsigned i=0;i<dd.mpi_request_index.size();i++) dd.mpi_request_index[i].wait();
+ int count=0;
+ for(std::set<int>::const_iterator p=unique.begin();p!=unique.end();++p){
+ if(dd.g2l[*p]>=0){
+ dd.indexToBeSent[count]=*p;
+ dd.positionsToBeSent[5*count+0]=positions[*p][0];
+ dd.positionsToBeSent[5*count+1]=positions[*p][1];
+ dd.positionsToBeSent[5*count+2]=positions[*p][2];
+ dd.positionsToBeSent[5*count+3]=masses[*p];
+ dd.positionsToBeSent[5*count+4]=charges[*p];
+ count++;
+ }
+ }
+ dd.mpi_request_positions.resize(dd.Get_size());
+ dd.mpi_request_index.resize(dd.Get_size());
+ for(int i=0;i<dd.Get_size();i++){
+ dd.mpi_request_index[i]=dd.Isend(&dd.indexToBeSent[0],count,i,666);
+ dd.mpi_request_positions[i]=dd.Isend(&dd.positionsToBeSent[0],5*count,i,667);
+ }
+ }
+}
+
+void Atoms::wait(){
+
+ if(dd && gatindex.size()<natoms){
+// receive toBeReceived
+ int count=0;
+ PlumedCommunicator::Status status;
+ for(int i=0;i<dd.Get_size();i++){
+ dd.Recv(&dd.indexToBeReceived[count],dd.indexToBeReceived.size()-count,i,666,status);
+ int c=status.Get_count<int>();
+ dd.Recv(&dd.positionsToBeReceived[5*count],dd.positionsToBeReceived.size()-5*count,i,667);
+ count+=c;
+ }
+ for(int i=0;i<count;i++){
+ positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[5*i+0];
+ positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[5*i+1];
+ positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[5*i+2];
+ masses[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+3];
+ charges[dd.indexToBeReceived[i]] =dd.positionsToBeReceived[5*i+4];
+ }
+ if(collectEnergy) dd.Sum(&energy,1);
+ forceOnEnergy=0.0;
+ }
+
+
+ for(unsigned i=0;i<requestset.size();i++){
+ if(!requestset[i]->isActive()) continue;
+ const vector<int> & indexes(requestset[i]->indexes);
+ vector<Vector> & p(requestset[i]->positions);
+ vector<double> & c(requestset[i]->charges);
+ vector<double> & m(requestset[i]->masses);
+ requestset[i]->box=box;
+ for(unsigned j=0;j<indexes.size();j++) p[j]=positions[indexes[j]];
+ for(unsigned j=0;j<indexes.size();j++) c[j]=charges[indexes[j]];
+ for(unsigned j=0;j<indexes.size();j++) m[j]=masses[indexes[j]];
+ };
+}
+
+void Atoms::updateForces(){
+ bool any(false);
+ virial.clear();
+ for(unsigned i=0;i<gatindex.size();i++) forces[gatindex[i]].clear();
+ for(unsigned i=0;i<requestset.size();i++){
+ if(!requestset[i]->isActive()) continue;
+ any=true;
+ const vector<int> & indexes(requestset[i]->indexes);
+ const vector<Vector> & f(requestset[i]->forces);
+ const Tensor & v(requestset[i]->virial);
+ if(!plumed.novirial) for(int l=0;l<3;l++)for(int m=0;m<3;m++) virial(l,m)+=v(l,m);
+ for(unsigned j=0;j<indexes.size();j++){
+ const unsigned iat=indexes[j];
+ forces[iat][0]+=f[j][0];
+ forces[iat][1]+=f[j][1];
+ forces[iat][2]+=f[j][2];
+ }
+ };
+ if(forceOnEnergy*forceOnEnergy>epsilon){
+ double alpha=1.0-forceOnEnergy;
+ mdatoms->rescaleForces(0,gatindex.size(),alpha);
+ }
+ if(!any)return;
+ mdatoms->updateForces(gatindex,forces);
+ if(dd.Get_rank()==0) mdatoms->updateVirial(virial);
+}
+
+void Atoms::setNatoms(int n){
+ natoms=n;
+ positions.resize(n);
+ forces.resize(n);
+ masses.resize(n);
+ charges.resize(n);
+ gatindex.resize(n);
+ for(unsigned i=0;i<gatindex.size();i++) gatindex[i]=i;
+}
+
+
+Atoms::Request::Request(Atoms& atoms,const vector<int>& indexes,
+ vector<double> & masses,
+ vector<double> & charges,
+ vector<Vector>& positions,
+ const vector<Vector>& forces,
+ Tensor&box,
+ const Tensor&virial):
+ active(false),
+ atoms(atoms),
+ indexes(indexes),
+ masses(masses),
+ charges(charges),
+ positions(positions),
+ forces(forces),
+ box(box),
+ virial(virial)
+{
+ for(unsigned i=0;i<indexes.size();i++) assert(indexes[i]<atoms.natoms);
+ unique.insert(indexes.begin(),indexes.end());
+ atoms.requestset.push_back(this);
+}
+
+Atoms::Request::~Request(){
+ vector<Request*>::iterator f=find(atoms.requestset.begin(),atoms.requestset.end(),this);
+ assert(f!=atoms.requestset.end());
+ atoms.requestset.erase(f);
+}
+
+void Atoms::DomainDecomposition::enable(PlumedCommunicator& c){
+ on=true;
+ Set_comm(c.Get_comm());
+}
+
+void Atoms::setAtomsNlocal(int n){
+ gatindex.resize(n);
+ if(dd){
+ dd.g2l.resize(natoms,-1);
+ dd.positionsToBeSent.resize(n*5,0.0);
+ dd.positionsToBeReceived.resize(natoms*5,0.0);
+ dd.indexToBeSent.resize(n,0);
+ dd.indexToBeReceived.resize(natoms,0);
+ };
+}
+
+void Atoms::setAtomsGatindex(int*g){
+ for(unsigned i=0;i<gatindex.size();i++) gatindex[i]=g[i];
+ for(unsigned i=0;i<dd.g2l.size();i++) dd.g2l[i]=-1;
+ if(dd) for(unsigned i=0;i<gatindex.size();i++) dd.g2l[gatindex[i]]=i;
+}
+
+void Atoms::setAtomsContiguous(int start){
+ for(unsigned i=0;i<gatindex.size();i++) gatindex[i]=start+i;
+ for(unsigned i=0;i<dd.g2l.size();i++) dd.g2l[i]=-1;
+ if(dd) for(unsigned i=0;i<gatindex.size();i++) dd.g2l[gatindex[i]]=i;
+}
+
+void Atoms::setRealPrecision(int p){
+ delete mdatoms;
+ mdatoms=MDAtomsBase::create(p);
+}
+
+int Atoms::getRealPrecision()const{
+ return mdatoms->getRealPrecision();
+}
+
+void Atoms::MD2double(const void*m,double&d)const{
+ assert(mdatoms); mdatoms->MD2double(m,d);
+}
+void Atoms::double2MD(const double&d,void*m)const{
+ assert(mdatoms); mdatoms->double2MD(d,m);
+}
+
+void Atoms::updateUnits(){
+ mdatoms->setUnits(internalLengthUnits/MDLengthUnits,internalEnergyUnits/MDEnergyUnits);
+}
+
+void Atoms::setTimeStep(void*p){
+ MD2double(p,timestep);
+}
+
+double Atoms::getTimeStep()const{
+ return timestep/internalTimeUnits*MDTimeUnits;
+}
+
+void Atoms::createFullList(int*n){
+ for(unsigned i=0;i<requestset.size();i++) if(requestset[i]->isActive())
+ fullList.insert(fullList.end(),requestset[i]->unique.begin(),requestset[i]->unique.end());
+ std::sort(fullList.begin(),fullList.end());
+ int nn=std::unique(fullList.begin(),fullList.end())-fullList.begin();
+ fullList.resize(nn);
+ *n=nn;
+}
+
+void Atoms::getFullList(int**x){
+ *x=&fullList[0];
+}
+
+void Atoms::clearFullList(){
+ fullList.resize(0);
+}
+
+void Atoms::init(){
+// Default: set domain decomposition to NO-decomposition, waiting for
+// further instruction
+ if(dd){
+ setAtomsNlocal(natoms);
+ setAtomsContiguous(0);
+ }
+}
+
+
+
+}
+
+
diff --git a/src/Atoms.h b/src/Atoms.h
new file mode 100644
index 000000000..141263150
--- /dev/null
+++ b/src/Atoms.h
@@ -0,0 +1,182 @@
+#ifndef __PLUMED_Atoms_h
+#define __PLUMED_Atoms_h
+#include <vector>
+#include <set>
+#include <cassert>
+#include <string>
+#include "PlumedCommunicator.h"
+#include "Tensor.h"
+#include "Pbc.h"
+
+namespace PLMD{
+
+class MDAtomsBase;
+class PlumedMain;
+
+/// Class containing atom related quantities from the MD code.
+class Atoms
+{
+ int natoms;
+ std::vector<Vector> positions;
+ std::vector<Vector> forces;
+ std::vector<double> masses;
+ std::vector<double> charges;
+ Tensor box;
+ Tensor virial;
+ double energy;
+ bool collectEnergy;
+
+ std::vector<int> fullList;
+
+ MDAtomsBase* mdatoms;
+ Pbc pbc;
+
+ PlumedMain & plumed;
+
+ double MDEnergyUnits,MDLengthUnits,MDTimeUnits;
+ double internalEnergyUnits,internalLengthUnits,internalTimeUnits;
+
+ double timestep;
+ double forceOnEnergy;
+
+
+public:
+
+ void forceEnergy(double d){forceOnEnergy+=d;};
+ double getEnergy()const{assert(collectEnergy);return energy;};
+ void setCollectEnergy(bool b){collectEnergy=b;};
+ void setMDEnergyUnits(double d){MDEnergyUnits=d;};
+ void setMDLengthUnits(double d){MDLengthUnits=d;};
+ void setMDTimeUnits(double d){MDTimeUnits=d;};
+ double getMDEnergyUnits()const{return MDEnergyUnits;};
+ double getMDLengthUnits()const{return MDLengthUnits;};
+ double getMDTimeUnits()const{return MDTimeUnits;};
+ void setInternalEnergyUnits(double d){internalEnergyUnits=d;};
+ void setInternalLengthUnits(double d){internalLengthUnits=d;};
+ void setInternalTimeUnits(double d){internalTimeUnits=d;};
+ double getInternalEnergyUnits()const{return internalEnergyUnits;};
+ double getInternalLengthUnits()const{return internalLengthUnits;};
+ double getInternalTimeUnits()const{return internalTimeUnits;};
+ void updateUnits();
+
+ void setTimeStep(void*);
+ double getTimeStep()const;
+
+ const Pbc& getPbc()const{return pbc;};
+
+ class Request{
+ friend class Atoms;
+ bool active;
+ Atoms& atoms;
+ const std::vector<int>& indexes;
+ std::vector<double>& masses;
+ std::vector<double>& charges;
+ std::vector<Vector> & positions;
+ const std::vector<Vector> & forces;
+ Tensor& box;
+ const Tensor& virial;
+ std::set<int> unique;
+ public:
+ void activate();
+ void deactivate();
+ bool isActive();
+ void setForced();
+ Request(Atoms& atoms,const std::vector<int>& indexes,
+ std::vector<double>& masses,
+ std::vector<double>& charges,
+ std::vector<Vector>& positions,
+ const std::vector<Vector>& forces,
+ Tensor& box,
+ const Tensor& virial);
+ ~Request();
+ };
+
+
+private:
+ std::vector<Request*> requestset;
+ typedef std::vector<Request*>::iterator requestsetIterator;
+ std::vector<int> gatindex;
+
+ class DomainDecomposition:
+ public PlumedCommunicator
+ {
+ public:
+ bool on;
+ std::vector<int> g2l;
+
+ std::vector<PlumedCommunicator::Request> mpi_request_positions;
+ std::vector<PlumedCommunicator::Request> mpi_request_index;
+
+ std::vector<double> positionsToBeSent;
+ std::vector<double> positionsToBeReceived;
+ std::vector<int> indexToBeSent;
+ std::vector<int> indexToBeReceived;
+ operator bool(){return on;};
+ DomainDecomposition():
+ on(false)
+ {};
+ void enable(PlumedCommunicator& c);
+ };
+
+ DomainDecomposition dd;
+
+public:
+ Atoms(PlumedMain&plumed);
+ ~Atoms();
+ void init();
+ void setNatoms(int);
+ const int & getNatoms()const;
+ void updateForces();
+ void setDomainDecomposition(PlumedCommunicator&);
+ void setAtomsGatindex(int*);
+ void setAtomsContiguous(int);
+ void setAtomsNlocal(int);
+
+ void setBox(void*);
+ void setPositions(void*);
+ void setPositions(void*,int);
+ void setMasses(void*);
+ void setCharges(void*);
+ void setVirial(void*);
+ void setForces(void*);
+ void setForces(void*,int);
+ void setEnergy(void*);
+
+ void share();
+ void wait();
+ void MD2double(const void*m,double&d)const;
+ void double2MD(const double&d,void*m)const;
+ void setRealPrecision(int);
+ int getRealPrecision()const;
+ void createFullList(int*);
+ void getFullList(int**);
+ void clearFullList();
+};
+
+inline
+const int & Atoms::getNatoms()const{
+ return natoms;
+}
+
+inline
+void Atoms::setDomainDecomposition(PlumedCommunicator& comm){
+ dd.enable(comm);
+}
+
+inline
+void Atoms::Request::activate(){
+ active=true;
+}
+
+inline
+void Atoms::Request::deactivate(){
+ active=false;
+}
+
+inline
+bool Atoms::Request::isActive(){
+ return active;
+}
+
+}
+#endif
diff --git a/src/Bias.cpp b/src/Bias.cpp
new file mode 100644
index 000000000..01631632a
--- /dev/null
+++ b/src/Bias.cpp
@@ -0,0 +1,24 @@
+#include "Bias.h"
+#include "Colvar.h"
+#include <cassert>
+
+using namespace PLMD;
+using namespace std;
+
+Bias::Bias(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+ActionWithValue(ao),
+ActionWithArguments(ao),
+outputForces(getArguments().size(),0.0)
+{
+}
+
+
+void Bias::apply(){
+ if(onStep()) for(unsigned i=0;i<getNumberOfArguments();++i){
+ getArguments()[i]->addForce(getStride()*outputForces[i]);
+ }
+}
+
+
diff --git a/src/Bias.h b/src/Bias.h
new file mode 100644
index 000000000..3b1ef3902
--- /dev/null
+++ b/src/Bias.h
@@ -0,0 +1,40 @@
+#ifndef __PLUMED_Bias_h
+#define __PLUMED_Bias_h
+
+#include "ActionPilot.h"
+#include "ActionWithValue.h"
+#include "ActionWithArguments.h"
+
+#define PLUMED_BIAS_INIT(ao) Action(ao),Bias(ao)
+
+namespace PLMD{
+
+/// Action defining a bias which can act on other Action's
+class Bias :
+ public ActionPilot,
+ public ActionWithValue,
+ public ActionWithArguments
+{
+ std::vector<double> outputForces;
+protected:
+ void resetOutputForces();
+ void setOutputForces(int i,double g);
+public:
+ Bias(const ActionOptions&ao);
+ void apply();
+};
+
+inline
+void Bias::setOutputForces(int i,double f){
+ outputForces[i]=f;
+}
+
+inline
+void Bias::resetOutputForces(){
+ for(unsigned i=0;i<outputForces.size();++i) outputForces[i]=0.0;
+}
+
+}
+
+#endif
+
diff --git a/src/BiasMovingRestraint.cpp b/src/BiasMovingRestraint.cpp
new file mode 100644
index 000000000..0347b1f31
--- /dev/null
+++ b/src/BiasMovingRestraint.cpp
@@ -0,0 +1,116 @@
+#include "Bias.h"
+#include "ActionRegister.h"
+
+#include <cassert>
+
+using namespace std;
+
+
+namespace PLMD{
+
+//+PLUMEDOC BIAS MOVINGRESTRAINT
+/**
+Moving restraint
+
+Similar to \ref RESTRAINT but can be moved during the simulation
+
+\par Syntax
+
+Example
+\verbatim
+MOVINGRESTRAINT
+\endverbatim
+
+If you use this variable, please cite the following work ... ... ...
+
+*/
+//+ENDPLUMEDOC
+
+
+class BiasMovingRestraint : public Bias{
+ std::vector<std::vector<double> > at;
+ std::vector<std::vector<double> > kappa;
+ std::vector<int> step;
+public:
+ BiasMovingRestraint(const ActionOptions&);
+ void calculate();
+};
+
+PLUMED_REGISTER_ACTION(BiasMovingRestraint,"MOVINGRESTRAINT")
+
+BiasMovingRestraint::BiasMovingRestraint(const ActionOptions&ao):
+PLUMED_BIAS_INIT(ao)
+{
+ for(int i=0;;i++){
+ int ss=-1;
+ std::vector<double> kk,aa;
+ string s;
+ Tools::convert(i,s);
+ parse("STEP"+s,ss);
+ if(ss<0) break;
+ for(unsigned j=0;j<step.size();j++) assert(ss>step[j]);
+ step.push_back(ss);
+ parseVector("KAPPA"+s,kk);
+ if(kk.size()==0 && i>0) kk=kappa[i-1];
+ assert(kk.size()==getNumberOfArguments());
+ kappa.push_back(kk);
+ parseVector("AT"+s,aa);
+ if(at.size()==0 && i>0) aa=at[i-1];
+ assert(aa.size()==getNumberOfArguments());
+ at.push_back(aa);
+ }
+ checkRead();
+
+ for(unsigned i=0;i<step.size();i++){
+ log.printf(" step%d %d\n",i,step[i]);
+ log.printf(" at");
+ for(unsigned j=0;j<at[i].size();j++) log.printf(" %f",at[i][j]);
+ log.printf("\n");
+ log.printf(" with force constant");
+ for(unsigned j=0;j<kappa[i].size();j++) log.printf(" %f",kappa[i][j]);
+ log.printf("\n");
+ };
+
+ addValue("");
+ addValue("Energy");
+ addValue("Force2");
+ addValue("Work");
+}
+
+
+void BiasMovingRestraint::calculate(){
+ double ene=0.0;
+ double totf2=0.0;
+ unsigned narg=getNumberOfArguments();
+ int now=getStep();
+ std::vector<double> kk(narg),aa(narg);
+ if(now<=step[0]){
+ kk=kappa[0];
+ aa=at[0];
+ } else if(now>=step[step.size()-1]){
+ kk=kappa[step.size()-1];
+ aa=at[step.size()-1];
+ } else {
+ unsigned i=0;
+ for(i=1;i<step.size();i++) if(now<step[i]) break;
+ double c2=(now-step[i-1])/double(step[i]-step[i-1]);
+ double c1=1.0-c2;
+ for(unsigned j=0;j<narg;j++) kk[j]=(c1*kappa[i-1][j]+c2*kappa[i][j]);
+ for(unsigned j=0;j<narg;j++) aa[j]=(c1*at[i-1][j]+c2*at[i][j]);
+ }
+ for(unsigned i=0;i<narg;++i){
+ const double cv=(getArgument(i)-aa[i]);
+ const double k=kk[i];
+ const double f=-k*cv;
+ ene+=0.5*k*cv*cv;
+ setOutputForces(i,f);
+ totf2+=f*f;
+ };
+ getValue("")->setValue(ene);
+ getValue("Energy")->setValue(ene);
+ getValue("Force2")->setValue(totf2);
+}
+
+}
+
+
diff --git a/src/BiasRestraint.cpp b/src/BiasRestraint.cpp
new file mode 100644
index 000000000..0483b06c8
--- /dev/null
+++ b/src/BiasRestraint.cpp
@@ -0,0 +1,85 @@
+#include "Bias.h"
+#include "ActionRegister.h"
+
+#include <cassert>
+
+using namespace std;
+
+
+namespace PLMD{
+
+//+PLUMEDOC BIAS RESTRAINT
+/**
+Harmonic restraint
+
+This bias imposes an harmonic restraint on one or more
+collective variables (or function). Besides the
+usual STRIDE, ARG and LABEL, it accepts the following
+keywords:
+- KAPPA an array of force constants (in PLUMED units)
+- AT an array defining the center of the restraint
+Example
+\verbatim
+DISTANCE ATOMS=5,10 LABEL=d1
+DISTANCE ATOMS=6,11 LABEL=d2
+DISTANCE ATOMS=7,12 LABEL=d3
+RESTRAINT ARG=d1,d2,d3 KAPPA=0.1,0.1,0.5 AT=5.0,6.0,7.0
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+class BiasRestraint : public Bias{
+ std::vector<double> at;
+ std::vector<double> kappa;
+public:
+ BiasRestraint(const ActionOptions&);
+ void calculate();
+};
+
+PLUMED_REGISTER_ACTION(BiasRestraint,"RESTRAINT")
+
+BiasRestraint::BiasRestraint(const ActionOptions&ao):
+PLUMED_BIAS_INIT(ao),
+at(0),
+kappa(getNumberOfArguments(),0.0)
+{
+ parseVector("KAPPA",kappa);
+ assert(kappa.size()==getNumberOfArguments());
+ parseVector("AT",at);
+ assert(at.size()==getNumberOfArguments());
+ checkRead();
+
+ log.printf(" at");
+ for(unsigned i=0;i<at.size();i++) log.printf(" %f",at[i]);
+ log.printf("\n");
+ log.printf(" with force constant");
+ for(unsigned i=0;i<kappa.size();i++) log.printf(" %f",kappa[i]);
+ log.printf("\n");
+
+ addValue("");
+ addValue("Energy");
+ addValue("Force2");
+}
+
+
+void BiasRestraint::calculate(){
+ double ene=0.0;
+ double totf2=0.0;
+ for(unsigned i=0;i<getNumberOfArguments();++i){
+ const double cv=(getArgument(i)-at[i]);
+ const double k=kappa[i];
+ const double f=-k*cv;
+ ene+=0.5*k*cv*cv;
+ setOutputForces(i,f);
+ totf2+=f*f;
+ };
+ setValue(ene);
+ Value* value;
+ value=getValue("Energy"); setValue(value,ene);
+ value=getValue("Force2"); setValue(value,totf2);
+}
+
+}
+
+
diff --git a/src/Colvar.cpp b/src/Colvar.cpp
new file mode 100644
index 000000000..09d42ad50
--- /dev/null
+++ b/src/Colvar.cpp
@@ -0,0 +1,61 @@
+#include "Colvar.h"
+#include "PlumedMain.h"
+#include <vector>
+#include <string>
+#include <cassert>
+
+using namespace std;
+using namespace PLMD;
+
+Colvar::Colvar(const ActionOptions&ao):
+Action(ao),
+ActionAtomistic(ao),
+ActionWithValue(ao),
+isEnergy(false)
+{
+}
+
+
+void Colvar::requestAtoms(vector<int> & a){
+ ActionAtomistic::requestAtoms(a);
+ setNumberOfParameters(3*a.size()+9);
+}
+
+void Colvar::apply(){
+ vector<Vector>& f(modifyForces());
+ Tensor& v(modifyVirial());
+
+ for(unsigned i=0;i<f.size();i++){
+ f[i][0]=0.0;
+ f[i][1]=0.0;
+ f[i][2]=0.0;
+ }
+ v.clear();
+
+ if(!isEnergy)
+ for(int i=0;i<getNumberOfValues();++i){
+ const vector<double> & derivatives(getValue(i)->getDerivatives());
+ const unsigned nat=f.size();
+ const double force=getValue(i)->getForce();
+ for(unsigned j=0;j<nat;++j){
+ f[j][0]+=force*derivatives[3*j+0];
+ f[j][1]+=force*derivatives[3*j+1];
+ f[j][2]+=force*derivatives[3*j+2];
+ }
+ v(0,0)+=force*derivatives[3*nat+0];
+ v(0,1)+=force*derivatives[3*nat+1];
+ v(0,2)+=force*derivatives[3*nat+2];
+ v(1,0)+=force*derivatives[3*nat+3];
+ v(1,1)+=force*derivatives[3*nat+4];
+ v(1,2)+=force*derivatives[3*nat+5];
+ v(2,0)+=force*derivatives[3*nat+6];
+ v(2,1)+=force*derivatives[3*nat+7];
+ v(2,2)+=force*derivatives[3*nat+8];
+ }
+ if(isEnergy) plumed.getAtoms().forceEnergy(getValue(0)->getForce());
+}
+
+
+
+
+
diff --git a/src/Colvar.h b/src/Colvar.h
new file mode 100644
index 000000000..8bb1e2a4f
--- /dev/null
+++ b/src/Colvar.h
@@ -0,0 +1,86 @@
+#ifndef __PLUMED_Colvar_h
+#define __PLUMED_Colvar_h
+#include <vector>
+#include <string>
+#include "ActionAtomistic.h"
+#include "ActionWithValue.h"
+
+#define PLUMED_COLVAR_INIT(ao) Action(ao),Colvar(ao)
+
+namespace PLMD {
+
+/// Action representing a collective variable
+class Colvar :
+ public ActionAtomistic,
+ public ActionWithValue
+ {
+protected:
+ bool isEnergy;
+ void requestAtoms(std::vector<int> & a);
+// These are so as to map to 3d vectors for atoms:
+ void setAtomsDerivatives(int,const Vector&);
+ void setAtomsDerivatives(Value*,int,const Vector&);
+ void setBoxDerivatives(const Tensor&);
+ void setBoxDerivatives(Value*,const Tensor&);
+ void setColvarValue(double);
+ void setColvarValue(Value*,double);
+public:
+ const Tensor & getBoxDerivatives()const;
+ const double & getForce()const;
+ void apply();
+
+
+public:
+
+
+ bool checkIsEnergy(){return isEnergy;};
+ Colvar(const ActionOptions&);
+ ~Colvar(){};
+
+};
+
+
+inline
+void Colvar::setAtomsDerivatives(int i,const Vector&d){
+ getValue(0)->setDerivatives(3*i+0,d[0]);
+ getValue(0)->setDerivatives(3*i+1,d[1]);
+ getValue(0)->setDerivatives(3*i+2,d[2]);
+}
+
+inline
+void Colvar::setAtomsDerivatives(Value*v,int i,const Vector&d){
+ v->setDerivatives(3*i+0,d[0]);
+ v->setDerivatives(3*i+1,d[1]);
+ v->setDerivatives(3*i+2,d[2]);
+}
+
+
+inline
+void Colvar::setBoxDerivatives(const Tensor&d){
+ getValue(0)->setDerivatives(3*getNatoms()+0,d(0,0));
+ getValue(0)->setDerivatives(3*getNatoms()+1,d(0,1));
+ getValue(0)->setDerivatives(3*getNatoms()+2,d(0,2));
+ getValue(0)->setDerivatives(3*getNatoms()+3,d(1,0));
+ getValue(0)->setDerivatives(3*getNatoms()+4,d(1,1));
+ getValue(0)->setDerivatives(3*getNatoms()+5,d(1,2));
+ getValue(0)->setDerivatives(3*getNatoms()+6,d(2,0));
+ getValue(0)->setDerivatives(3*getNatoms()+7,d(2,1));
+ getValue(0)->setDerivatives(3*getNatoms()+8,d(2,2));
+}
+
+inline
+void Colvar::setBoxDerivatives(Value* v,const Tensor&d){
+ v->setDerivatives(3*getNatoms()+0,d(0,0));
+ v->setDerivatives(3*getNatoms()+1,d(0,1));
+ v->setDerivatives(3*getNatoms()+2,d(0,2));
+ v->setDerivatives(3*getNatoms()+3,d(1,0));
+ v->setDerivatives(3*getNatoms()+4,d(1,1));
+ v->setDerivatives(3*getNatoms()+5,d(1,2));
+ v->setDerivatives(3*getNatoms()+6,d(2,0));
+ v->setDerivatives(3*getNatoms()+7,d(2,1));
+ v->setDerivatives(3*getNatoms()+8,d(2,2));
+}
+
+}
+
+#endif
diff --git a/src/ColvarDistance.cpp b/src/ColvarDistance.cpp
new file mode 100644
index 000000000..870574081
--- /dev/null
+++ b/src/ColvarDistance.cpp
@@ -0,0 +1,119 @@
+#include "Colvar.h"
+#include "ActionRegister.h"
+
+#include <string>
+#include <cmath>
+#include <cassert>
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC COLVAR DISTANCE
+/**
+Calculate the distance between two atoms.
+
+\par Syntax
+DISTANCE ATOMS=x,y [COMPONENTS] [PBC]
+If the COMPONENTS flag is present, the three components of the distance
+can be accessed respectively as .x .y and .z.
+If the PBC flag is present, distance is computed using periodic boundary conditions.
+
+\par Example
+The following input is printing the distance between atoms 3 and 5,
+the distance between atoms 2 and 4 and its x component.
+\verbatim
+DISTANCE ATOMS=3,5 LABEL=d1
+DISTANCE ATOMS=2,4 COMPONENTS LABEL=d2
+PRINT ARG=d1,d2,d2.x
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+class ColvarDistance : public Colvar {
+ bool components;
+ bool pbc;
+
+public:
+ ColvarDistance(const ActionOptions&);
+// active methods:
+ virtual void calculate();
+};
+
+PLUMED_REGISTER_ACTION(ColvarDistance,"DISTANCE")
+
+ColvarDistance::ColvarDistance(const ActionOptions&ao):
+PLUMED_COLVAR_INIT(ao),
+components(false),
+pbc(true)
+{
+ vector<int> atoms;
+ parseVector("ATOMS",atoms);
+ assert(atoms.size()==2);
+ parseFlag("COMPONENTS",components);
+ bool nopbc=!pbc;
+ parseFlag("NOPBC",nopbc);
+ pbc=!nopbc;
+ parseFlag("PBC",pbc);
+ checkRead();
+
+ log.printf(" between atoms %d %d\n",atoms[0],atoms[1]);
+ if(pbc) log.printf(" using periodic boundary conditions\n");
+ else log.printf(" without periodic boundary conditions\n");
+
+ addValueWithDerivatives("");
+
+ if(components){
+ addValueWithDerivatives("x");
+ addValueWithDerivatives("y");
+ addValueWithDerivatives("z");
+ }
+
+ requestAtoms(atoms);
+}
+
+
+// calculator
+void ColvarDistance::calculate(){
+
+ Vector distance;
+ if(pbc){
+ distance=pbcDistance(getPositions(0),getPositions(1));
+ } else {
+ distance=delta(getPositions(0),getPositions(1));
+ }
+ const double value=distance.modulo();
+ const double invvalue=1.0/value;
+
+ setAtomsDerivatives(0,-invvalue*distance);
+ setAtomsDerivatives(1,invvalue*distance);
+ setBoxDerivatives (-invvalue*Tensor(distance,distance));
+ setValue (value);
+
+ if(components){
+ Value* valuex=getValue("x");
+ Value* valuey=getValue("y");
+ Value* valuez=getValue("z");
+
+ setAtomsDerivatives (valuex,0,Vector(-1,0,0));
+ setAtomsDerivatives (valuex,1,Vector(+1,0,0));
+ setBoxDerivatives (valuex,Tensor(distance,Vector(-1,0,0)));
+ setValue (valuex,distance[0]);
+
+ setAtomsDerivatives (valuey,0,Vector(0,-1,0));
+ setAtomsDerivatives (valuey,1,Vector(0,+1,0));
+ setBoxDerivatives (valuey,Tensor(distance,Vector(0,-1,0)));
+ setValue (valuey,distance[1]);
+
+ setAtomsDerivatives (valuez,0,Vector(0,0,-1));
+ setAtomsDerivatives (valuez,1,Vector(0,0,+1));
+ setBoxDerivatives (valuez,Tensor(distance,Vector(0,0,-1)));
+ setValue (valuez,distance[2]);
+ };
+}
+
+}
+
+
+
diff --git a/src/ColvarEnergy.cpp b/src/ColvarEnergy.cpp
new file mode 100644
index 000000000..0c91c0d0c
--- /dev/null
+++ b/src/ColvarEnergy.cpp
@@ -0,0 +1,58 @@
+#include "Colvar.h"
+#include "ActionRegister.h"
+#include "PlumedMain.h"
+
+#include <string>
+#include <cmath>
+#include <cassert>
+
+namespace PLMD{
+
+//+PLUMEDOC COLVAR ENERGY
+/**
+Potential energy of the system. Example:
+\verbatim
+ENERGY LABEL=energy
+\endverbatim
+
+\bug It does not work with variable cell simulations. Should include also PV contribution.
+
+*/
+//+ENDPLUMEDOC
+
+
+class ColvarEnergy : public Colvar {
+ bool components;
+
+public:
+ ColvarEnergy(const ActionOptions&);
+// active methods:
+ virtual void calculate();
+};
+
+
+using namespace std;
+
+
+PLUMED_REGISTER_ACTION(ColvarEnergy,"ENERGY")
+
+ColvarEnergy::ColvarEnergy(const ActionOptions&ao):
+PLUMED_COLVAR_INIT(ao),
+components(false)
+{
+ std::vector<int> atoms;
+ requestAtoms(atoms);
+ isEnergy=true;
+ addValueWithDerivatives("");
+}
+
+
+// calculator
+void ColvarEnergy::calculate(){
+ setValue(plumed.getAtoms().getEnergy());
+}
+
+}
+
+
+
diff --git a/src/ColvarTemplate.cpp b/src/ColvarTemplate.cpp
new file mode 100644
index 000000000..6b4cc868a
--- /dev/null
+++ b/src/ColvarTemplate.cpp
@@ -0,0 +1,118 @@
+#include "Colvar.h"
+#include "ActionRegister.h"
+
+#include <string>
+#include <cmath>
+#include <cassert>
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC COLVAR TEMPLATE
+/**
+Calculate distance between two atoms
+
+\author Giovanni Bussi
+\date 17-12-2010
+
+\par Syntax
+
+TEMPLATE ATOMS=x,y [COMPONENTS] [PBC]
+
+Example
+\verbatim
+TEMPLATE ATOMS=3,5
+\endverbatim
+
+If you use this variable, please cite the following work ... ... ...
+
+*/
+//+ENDPLUMEDOC
+
+class ColvarTemplate : public Colvar {
+ bool components;
+ bool pbc;
+
+public:
+ ColvarTemplate(const ActionOptions&);
+// active methods:
+ virtual void calculate();
+};
+
+PLUMED_REGISTER_ACTION(ColvarTemplate,"TEMPLATE")
+
+ColvarTemplate::ColvarTemplate(const ActionOptions&ao):
+PLUMED_COLVAR_INIT(ao),
+components(false),
+pbc(true)
+{
+ vector<int> atoms;
+ parseVector("ATOMS",atoms);
+ assert(atoms.size()==2);
+ parseFlag("COMPONENTS",components);
+ bool nopbc=!pbc;
+ parseFlag("NOPBC",nopbc);
+ pbc=!nopbc;
+ parseFlag("PBC",pbc);
+ checkRead();
+
+ log.printf(" between atoms %d %d\n",atoms[0],atoms[1]);
+ if(pbc) log.printf(" using periodic boundary conditions\n");
+ else log.printf(" without periodic boundary conditions\n");
+
+ addValueWithDerivatives("");
+
+ if(components){
+ addValueWithDerivatives("x");
+ addValueWithDerivatives("y");
+ addValueWithDerivatives("z");
+ }
+
+ requestAtoms(atoms);
+}
+
+
+// calculator
+void ColvarTemplate::calculate(){
+
+ Vector distance;
+ if(pbc){
+ distance=pbcDistance(getPositions(0),getPositions(1));
+ } else {
+ distance=delta(getPositions(0),getPositions(1));
+ }
+ const double value=distance.modulo();
+ const double invvalue=1.0/value;
+
+ setAtomsDerivatives(0,-invvalue*distance);
+ setAtomsDerivatives(1,invvalue*distance);
+ setBoxDerivatives (-invvalue*Tensor(distance,distance));
+ setValue (value);
+
+ if(components){
+ Value* valuex=getValue("x");
+ Value* valuey=getValue("y");
+ Value* valuez=getValue("z");
+
+ setAtomsDerivatives (valuex,0,Vector(-1,0,0));
+ setAtomsDerivatives (valuex,1,Vector(+1,0,0));
+ setBoxDerivatives (valuex,Tensor(distance,Vector(-1,0,0)));
+ setValue (valuex,distance[0]);
+
+ setAtomsDerivatives (valuey,0,Vector(0,-1,0));
+ setAtomsDerivatives (valuey,1,Vector(0,+1,0));
+ setBoxDerivatives (valuey,Tensor(distance,Vector(0,-1,0)));
+ setValue (valuey,distance[1]);
+
+ setAtomsDerivatives (valuez,0,Vector(0,0,-1));
+ setAtomsDerivatives (valuez,1,Vector(0,0,+1));
+ setBoxDerivatives (valuez,Tensor(distance,Vector(0,0,-1)));
+ setValue (valuez,distance[2]);
+ };
+}
+
+}
+
+
+
diff --git a/src/ColvarVolume.cpp b/src/ColvarVolume.cpp
new file mode 100644
index 000000000..d702eed0c
--- /dev/null
+++ b/src/ColvarVolume.cpp
@@ -0,0 +1,62 @@
+#include "Colvar.h"
+#include "ActionRegister.h"
+
+#include <string>
+#include <cmath>
+#include <cassert>
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC COLVAR VOLUME
+/**
+Volume of the simulation box. Example:
+\verbatim
+VOLUME LABEL=volume
+\endverbatim
+*/
+//+ENDPLUMEDOC
+
+
+class ColvarVolume : public Colvar {
+ bool components;
+
+public:
+ ColvarVolume(const ActionOptions&);
+// active methods:
+ virtual void calculate();
+};
+
+PLUMED_REGISTER_ACTION(ColvarVolume,"VOLUME")
+
+ColvarVolume::ColvarVolume(const ActionOptions&ao):
+PLUMED_COLVAR_INIT(ao),
+components(false)
+{
+ std::vector<int> atoms;
+ parseFlag("COMPONENTS",components);
+ checkRead();
+
+ if(components){
+// todo
+ }
+ addValueWithDerivatives("");
+ requestAtoms(atoms);
+}
+
+
+// calculator
+void ColvarVolume::calculate(){
+ if(components){
+// todo
+ };
+
+ setBoxDerivatives(-1.0*Tensor::identity());
+ setValue (getBox().determinant());
+}
+
+}
+
+
+
diff --git a/src/Debug.cpp b/src/Debug.cpp
new file mode 100644
index 000000000..d8c0c5b40
--- /dev/null
+++ b/src/Debug.cpp
@@ -0,0 +1,73 @@
+#include "ActionRegister.h"
+#include "ActionPilot.h"
+#include "PlumedMain.h"
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC GENERIC DEBUG
+/**
+ Action to set some debug flags
+
+ This action can be used to enable debug options.
+ It accepts a STRIDE option as the \ref Bias actions,
+ which is used for debug options which are repeated
+ along the simulation.
+ It accepts the following flags:
+- logActivity: writes (every STRIDE steps) the list
+ of which actions are active and which ar inactive in the
+ plumed log, in term of a sequence of + (active) and - (inactive)
+- NOVIRIAL: switches off (for the entire simulation) the contribution
+ of virial computed in plumed
+*/
+//+ENDPLUMEDOC
+class Debug:
+ public ActionPilot
+{
+ bool logActivity;
+ bool novirial;
+public:
+ Debug(const ActionOptions&ao);
+ void calculate(){};
+ void apply();
+};
+
+PLUMED_REGISTER_ACTION(Debug,"DEBUG")
+
+Debug::Debug(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+logActivity(false),
+novirial(false){
+ parseFlag("logActivity",logActivity);
+ if(logActivity) log.printf(" logging activity\n");
+ parseFlag("NOVIRIAL",novirial);
+ if(novirial) log.printf(" Switching off virial contribution\n");
+ if(novirial) plumed.novirial=true;
+ checkRead();
+}
+
+void Debug::apply(){
+ if(logActivity){
+ const ActionSet&actionSet(plumed.getActionSet());
+ int a=0;
+ for(ActionSet::const_iterator p=actionSet.begin();p!=actionSet.end();++p){
+ if(dynamic_cast<Debug*>(*p))continue;
+ if((*p)->isActive()) a++;
+ };
+ if(a>0){
+ log.printf("activity at step %i: ",getStep());
+ for(ActionSet::const_iterator p=actionSet.begin();p!=actionSet.end();++p){
+ if(dynamic_cast<Debug*>(*p))continue;
+ if((*p)->isActive()) log.printf("+");
+ else log.printf("-");
+ };
+ log.printf("\n");
+ };
+ };
+
+}
+
+}
+
diff --git a/src/Flush.cpp b/src/Flush.cpp
new file mode 100644
index 000000000..60c31c09f
--- /dev/null
+++ b/src/Flush.cpp
@@ -0,0 +1,45 @@
+#include "ActionRegister.h"
+#include "ActionPilot.h"
+#include "PlumedMain.h"
+
+namespace PLMD{
+
+using namespace std;
+
+//+PLUMEDOC GENERIC FLUSH
+/**
+Periodically flush open files.
+
+This Action is used to flush the open files periodically.
+Similarly the other Actions, it understands the keyword STRIDE,
+which is the number of timesteps between flushings
+\verbatim
+# This is flushing all output files every 100 steps
+FLUSH STRIDE=100
+\endverbatim
+*/
+//+ENDPLUMEDOC
+
+class Flush:
+ public ActionPilot
+{
+public:
+ Flush(const ActionOptions&ao):
+ Action(ao),
+ ActionPilot(ao)
+ {
+ checkRead();
+ }
+ void calculate(){};
+ void apply(){
+ const ActionSet & actionSet(plumed.getActionSet());
+ for(ActionSet::const_iterator p=actionSet.begin();p!=actionSet.end();++p)
+ (*p)->flush();
+ }
+};
+
+PLUMED_REGISTER_ACTION(Flush,"FLUSH")
+
+}
+
+
diff --git a/src/Function.cpp b/src/Function.cpp
new file mode 100644
index 000000000..0b4184717
--- /dev/null
+++ b/src/Function.cpp
@@ -0,0 +1,31 @@
+#include "Function.h"
+#include "Colvar.h"
+#include <cassert>
+
+using namespace PLMD;
+using namespace std;
+
+Function::Function(const ActionOptions&ao):
+Action(ao),
+ActionWithValue(ao),
+ActionWithArguments(ao)
+{
+ setNumberOfParameters(getNumberOfArguments());
+}
+
+void Function::apply(){
+ vector<double> f(getNumberOfArguments(),0.0);
+
+ for(int i=0;i<getNumberOfValues();++i){
+ const vector<double> & derivatives(getValue(i)->getDerivatives());
+ for(unsigned j=0;j<derivatives.size();j++){
+ f[j]+=getForce(i)*derivatives[j];
+ }
+ }
+ for(unsigned i=0;i<getNumberOfArguments();++i){
+ getArguments()[i]->addForce(f[i]);
+ }
+}
+
+
+
diff --git a/src/Function.h b/src/Function.h
new file mode 100644
index 000000000..c440c8357
--- /dev/null
+++ b/src/Function.h
@@ -0,0 +1,35 @@
+#ifndef __PLUMED_Function_h
+#define __PLUMED_Function_h
+
+#include "ActionWithValue.h"
+#include "ActionWithArguments.h"
+
+namespace PLMD{
+
+/// Action representing a function of other actions
+class Function:
+ public ActionWithValue,
+ public ActionWithArguments
+{
+public:
+ Function(const ActionOptions&);
+ virtual ~Function(){};
+ void apply();
+ void setDerivatives(int,double);
+ void setDerivatives(Value*,int,double);
+};
+
+inline
+void Function::setDerivatives(int i,double d){
+ getValue(0)->setDerivatives(i,d);
+}
+
+inline
+void Function::setDerivatives(Value*v,int i,double d){
+ v->setDerivatives(i,d);
+}
+
+}
+
+#endif
+
diff --git a/src/FunctionCombine.cpp b/src/FunctionCombine.cpp
new file mode 100644
index 000000000..0d2c562cd
--- /dev/null
+++ b/src/FunctionCombine.cpp
@@ -0,0 +1,67 @@
+#include "ActionRegister.h"
+#include "Function.h"
+
+#include <cmath>
+#include <cassert>
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC FUNCTION COMBINE
+/**
+Combinatin of more CVs
+
+\par Syntax
+
+
+*/
+//+ENDPLUMEDOC
+
+
+class FunctionCombine :
+ public Function
+{
+ std::vector<double> coefficients;
+ std::vector<double> powers;
+public:
+ FunctionCombine(const ActionOptions&);
+ void calculate();
+};
+
+
+PLUMED_REGISTER_ACTION(FunctionCombine,"COMBINE")
+
+FunctionCombine::FunctionCombine(const ActionOptions&ao):
+Action(ao),
+Function(ao),
+coefficients(getNumberOfArguments(),1.0),
+powers(getNumberOfArguments(),1.0)
+{
+ parseVector("COEFFICIENTS",coefficients);
+ assert(coefficients.size()==static_cast<unsigned>(getNumberOfArguments()));
+ parseVector("POWERS",powers);
+ assert(powers.size()==static_cast<unsigned>(getNumberOfArguments()));
+ checkRead();
+
+ addValueWithDerivatives("");
+ log.printf(" with coefficients:");
+ for(unsigned i=0;i<coefficients.size();i++) log.printf(" %f",coefficients[i]);
+ log.printf("\n");
+ log.printf(" and powers:");
+ for(unsigned i=0;i<powers.size();i++) log.printf(" %f",powers[i]);
+ log.printf("\n");
+}
+
+void FunctionCombine::calculate(){
+ double combine=0.0;
+ for(unsigned i=0;i<coefficients.size();++i){
+ combine+=coefficients[i]*pow(getArgument(i),powers[i]);
+ setDerivatives(i,coefficients[i]*powers[i]*pow(getArgument(i),powers[i]-1.0));
+ };
+ setValue(combine);
+}
+
+}
+
+
diff --git a/src/FunctionMatheval.cpp b/src/FunctionMatheval.cpp
new file mode 100644
index 000000000..803827775
--- /dev/null
+++ b/src/FunctionMatheval.cpp
@@ -0,0 +1,111 @@
+#ifdef __PLUMED_HAS_MATHEVAL
+#include "ActionRegister.h"
+#include "Function.h"
+#include <cassert>
+#include <matheval.h>
+
+using namespace std;
+
+namespace PLMD{
+
+
+//+PLUMEDOC FUNCTION MATHEVAL
+/**
+Combination of more CVs using a matheval expression
+
+* VAR tells the names of the variables used in the FUNC string
+ If absent, the names are set to x,y,z. With more than 3 arguments explicit
+ names are compulsory
+* FUNC gives the function definition in matheval syntax
+
+\verbatim
+MATHEVAL LABEL=c1 ARG=distance1,distance2 VAR=a,b FUNC=(a+b)/10.0
+MATHEVAL LABEL=c2 ARG=distance1,distance2 FUNC=(x-y)/sin(y)
+\endverbatim
+
+
+*/
+//+ENDPLUMEDOC
+
+
+class FunctionMatheval :
+ public Function
+{
+ void* evaluator;
+ vector<void*> evaluator_deriv;
+ vector<string> var;
+ string func;
+ vector<double> values;
+ vector<char*> names;
+public:
+ FunctionMatheval(const ActionOptions&);
+ ~FunctionMatheval();
+ void calculate();
+};
+
+
+PLUMED_REGISTER_ACTION(FunctionMatheval,"MATHEVAL")
+
+FunctionMatheval::FunctionMatheval(const ActionOptions&ao):
+Action(ao),
+Function(ao),
+evaluator_deriv(getNumberOfArguments()),
+values(getNumberOfArguments()),
+names(getNumberOfArguments())
+{
+ parseVector("VAR",var);
+ if(var.size()==0){
+ var.resize(getNumberOfArguments());
+ assert(getNumberOfArguments()<=3);
+ if(var.size()>0) var[0]="x";
+ if(var.size()>1) var[1]="y";
+ if(var.size()>2) var[2]="z";
+ }
+ assert(var.size()==getNumberOfArguments());
+ parse("FUNC",func);
+ checkRead();
+
+ evaluator=evaluator_create(const_cast<char*>(func.c_str()));
+
+ char **check_names;
+ int check_count;
+ evaluator_get_variables(evaluator,&check_names,&check_count);
+ assert(check_count==int(getNumberOfArguments()));
+ for(unsigned i=0;i<getNumberOfArguments();i++){
+ bool found=false;
+ for(unsigned j=0;j<getNumberOfArguments();j++){
+ if(var[i]==check_names[j])found=true;
+ }
+ assert(found);
+ }
+
+ for(unsigned i=0;i<getNumberOfArguments();i++)
+ evaluator_deriv[i]=evaluator_derivative(evaluator,const_cast<char*>(var[i].c_str()));
+
+ addValueWithDerivatives("");
+
+ log.printf(" with function : %s\n",func.c_str());
+ log.printf(" with variables :");
+ for(unsigned i=0;i<var.size();i++) log.printf(" %s",var[i].c_str());
+ log.printf("\n");
+}
+
+void FunctionMatheval::calculate(){
+ for(unsigned i=0;i<getNumberOfArguments();i++) values[i]=getArgument(i);
+ for(unsigned i=0;i<getNumberOfArguments();i++) names[i]=const_cast<char*>(var[i].c_str());
+ setValue(evaluator_evaluate(evaluator,names.size(),&names[0],&values[0]));
+
+ for(unsigned i=0;i<getNumberOfArguments();i++){
+ setDerivatives(i,evaluator_evaluate(evaluator_deriv[i],names.size(),&names[0],&values[0]));
+ }
+}
+
+FunctionMatheval::~FunctionMatheval(){
+ evaluator_destroy(evaluator);
+ for(unsigned i=0;i<evaluator_deriv.size();i++)evaluator_destroy(evaluator_deriv[i]);
+}
+
+}
+
+#endif
+
diff --git a/src/IMD.cpp b/src/IMD.cpp
new file mode 100644
index 000000000..aae0cc1e6
--- /dev/null
+++ b/src/IMD.cpp
@@ -0,0 +1,252 @@
+#ifdef __PLUMED_HAS_IMD
+#include <unistd.h>
+
+#include "ActionRegister.h"
+#include "ActionAtomistic.h"
+#include "ActionPilot.h"
+#include "PlumedMain.h"
+
+extern "C" {
+#include "../imd/vmdsock.h"
+#include "../imd/imd.h"
+}
+
+
+namespace PLMD {
+
+//+PLUMEDOC GENERIC IMD
+/**
+Use interactive molecular dynamics with VMD
+
+\verbatim
+# listen to port 1112 of localhost
+IMD PORT=1112
+\endverbatim
+
+\verbatim
+# listen to port 1112 of pippo
+IMD HOST=pippo PORT=1112
+\endverbatim
+
+\verbatim
+# listen to port 1112 of localhost and run only when connected
+IMD PORT=1112 WAIT
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+class IMD :
+ public ActionAtomistic,
+ public ActionPilot
+ {
+ std::string host;
+ int port;
+ bool wait;
+ bool wrap;
+ void* sock;
+ void* clientsock;
+ bool connected;
+ std::vector<float> coord;
+ std::vector<double> forces;
+ int natoms;
+ int transferRate;
+ double fscale;
+ void connect();
+ void receive();
+ void sendCoordinates();
+public:
+ void calculate();
+ void apply();
+ IMD(const ActionOptions&);
+ ~IMD(){};
+};
+
+PLUMED_REGISTER_ACTION(IMD,"IMD")
+
+IMD::IMD(const ActionOptions& ao):
+ Action(ao),
+ ActionAtomistic(ao),
+ ActionPilot(ao),
+ host("localhost"),
+ port(0),
+ wait(false),
+ wrap(false),
+ sock(NULL),
+ clientsock(NULL),
+ connected(false),
+ transferRate(100),
+ fscale(1.0)
+{
+ natoms=plumed.getAtoms().getNatoms();
+
+ std::vector<int> index(natoms);
+ for(int i=0;i<natoms;i++) index[i]=i;
+ requestAtoms(index);
+ coord.resize(natoms*3,float(0.0));
+ forces.resize(natoms*3,0.0);
+
+ parseFlag("WAIT",wait);
+ bool nowait=false;
+ parseFlag("NOWAIT",nowait);
+ if(nowait)wait=false;
+ parseFlag("WRAP",wrap);
+ parse("PORT",port);
+ parse("HOST",host);
+ parse("FSCALE",fscale);
+
+ checkRead();
+
+ log.printf(" with host %s\n",host.c_str());
+ log.printf(" with port %d\n",port);
+ if(wait) log.printf(" waiting for a connection\n");
+ else log.printf(" not waiting for a connection\n");
+ if(wrap) log.printf(" wrapping atoms\n");
+ else log.printf(" not wrapping atoms\n");
+ log.printf(" WMD forces will be scaled by %f\n",fscale);
+
+ if(comm.Get_rank()==0){
+ vmdsock_init();
+ sock = vmdsock_create();
+ vmdsock_bind(sock, port);
+ vmdsock_listen(sock);
+ }
+
+ connect();
+}
+
+void IMD::connect(){
+ if(comm.Get_rank()==0) {
+ if(wait && clientsock==NULL)
+ fprintf(stderr,"Waiting for IMD connection on %s:%d...\n", host.c_str(), port);
+ do{
+ if (vmdsock_selread(sock,00) > 0) {
+ clientsock = vmdsock_accept(sock);
+ if (imd_handshake(clientsock)) {
+ clientsock = NULL;
+ };
+ sleep(1);
+ int length;
+ if(clientsock){
+ if (vmdsock_selread(clientsock, 0) != 1 ||
+ imd_recv_header(clientsock, &length) != IMD_GO) {
+ clientsock = NULL;
+ }
+ }
+ }
+ } while(wait && clientsock==NULL);
+ connected=(clientsock!=NULL);
+ int c=connected;
+ comm.Bcast(&c,1,0);
+ } else {
+ int c;
+ comm.Bcast(&c,1,0);
+ connected=c;
+ }
+}
+
+void IMD::receive(){
+
+ if(!connected) return;
+
+ if(clientsock){
+ IMDType type;
+ int length;
+ int itype;
+ while (vmdsock_selread(clientsock,0) > 0) {
+ type = imd_recv_header(clientsock, &length);
+ if(type==IMD_MDCOMM){
+ int32* vmd_atoms = new int32[length];
+ float* vmd_forces = new float[3*length];
+ imd_recv_mdcomm(clientsock, length, vmd_atoms, vmd_forces);
+ for(int i=0;i<length;i++){
+ forces[3*vmd_atoms[i]+0]=vmd_forces[3*i+0];
+ forces[3*vmd_atoms[i]+1]=vmd_forces[3*i+1];
+ forces[3*vmd_atoms[i]+2]=vmd_forces[3*i+2];
+ }
+ delete [] vmd_atoms;
+ delete [] vmd_forces;
+ itype=0;
+ comm.Bcast(&itype,1,0);
+ comm.Bcast(&forces[0],forces.size(),0);
+ }else if(type==IMD_DISCONNECT){
+ vmdsock_destroy(clientsock);
+ clientsock=NULL;
+ for(unsigned i=0;i<forces.size();i++) forces[i]=0.0;
+ connected=false;
+ itype=1;
+ comm.Bcast(&itype,1,0);
+ break;
+ }else if(type==IMD_TRATE){
+ if(length<1) length=1;
+ itype=2;
+ log.printf("IMD: setting transfer rate to %d\n",length);
+ transferRate=length;
+ comm.Bcast(&itype,1,0);
+ comm.Bcast(&transferRate,1,0);
+ }else if(type==IMD_KILL){
+ log.printf("IMD: killing simulation\n");
+ itype=3;
+ comm.Bcast(&itype,1,0);
+ plumed.exit();
+ }
+ }
+ itype=-1;
+ comm.Bcast(&itype,1,0);
+ }
+
+ if(comm.Get_rank()!=0){
+ int itype;
+ while(true){
+ comm.Bcast(&itype,1,0);
+ if(itype==-1)break;
+ else if(itype==0) comm.Bcast(&forces[0],forces.size(),0);
+ else if(itype==1) {
+ for(unsigned i=0;i<forces.size();i++) forces[i]=0.0;
+ connected=false;
+ }
+ else if(itype==2) comm.Bcast(&transferRate,1,0);
+ else if(itype==3) plumed.exit();
+ else assert(0);
+ }
+ }
+
+}
+
+void IMD::calculate(){
+ if(comm.Get_rank()==0 && connected && plumed.getStep()%transferRate==0 && vmdsock_selwrite(clientsock,0)) {
+ double scale=10.0*plumed.getAtoms().getInternalLengthUnits();
+ Vector ref;
+ for(int i=0;i<natoms;i++){
+ Vector pos=getPositions(i);
+ if(wrap) pos=pbcDistance(ref,pos);
+ coord[3*i+0]=static_cast<float>((pos[0]*scale));
+ coord[3*i+1]=static_cast<float>((pos[1]*scale));
+ coord[3*i+2]=static_cast<float>((pos[2]*scale));
+ }
+ imd_send_fcoords(clientsock,natoms,&coord[0]);
+ }
+}
+
+void IMD::apply(){
+
+ std::vector<Vector> & f(modifyForces());
+
+ const double scale=4.184/plumed.getAtoms().getInternalEnergyUnits()
+ /(0.1/plumed.getAtoms().getInternalLengthUnits())*fscale;
+
+ for(unsigned i=0;i<f.size();i++){
+ f[i][0]=forces[3*i+0]*getStride()*scale;
+ f[i][1]=forces[3*i+1]*getStride()*scale;
+ f[i][2]=forces[3*i+2]*getStride()*scale;
+ }
+
+ connect();
+ receive();
+
+}
+
+
+}
+
+#endif
diff --git a/src/Log.cpp b/src/Log.cpp
new file mode 100644
index 000000000..b72040669
--- /dev/null
+++ b/src/Log.cpp
@@ -0,0 +1,54 @@
+#include "Log.h"
+#include <cstdarg>
+#include <cassert>
+
+using namespace std;
+using namespace PLMD;
+
+int Log::printf(const char*fmt,...){
+ if(comm.Get_rank()>0)return 0;
+ int pointer=strlen(buffer);
+ va_list arg;
+ va_start(arg, fmt);
+ int r=vsnprintf(&buffer[pointer],buflen-pointer,fmt,arg);
+ va_end(arg);
+ assert(r>-1 && r<buflen-pointer);
+
+// Line is buffered until newline, then written with a PLUMED: prefix
+ char*p1=buffer;
+ char*p2;
+ while((p2=strchr(p1,'\n'))){
+ *p2='\0';
+ fprintf(fp,"PLUMED: %s\n",p1);
+ p1=p2+1;
+ };
+ memmove(buffer,p1,strlen(p1)+1);
+ return r;
+}
+
+Log::Log(PlumedCommunicator &comm):
+ fp(stdout),
+ toBeClosed(false),
+ comm(comm){
+ buffer=new char[buflen];
+ buffer[0]='\0';
+}
+
+Log::~Log(){
+ if(comm.Get_rank()>0)return;
+ if(!fp && toBeClosed)fclose(fp);
+ delete [] buffer;
+}
+
+void Log::setFile(string str){
+ if(comm.Get_rank()>0)return;
+ fp=fopen(str.c_str(),"w");
+ toBeClosed=true;
+}
+
+void Log::set(FILE*f){
+ if(comm.Get_rank()>0)return;
+ fp=f;
+}
+
+
diff --git a/src/Log.h b/src/Log.h
new file mode 100644
index 000000000..2a27ccb13
--- /dev/null
+++ b/src/Log.h
@@ -0,0 +1,53 @@
+#ifndef __PLUMED_Log_h
+#define __PLUMED_Log_h
+#include <cstdio>
+#include <string>
+#include <sstream>
+#include "PlumedCommunicator.h"
+
+namespace PLMD{
+
+/// Class containing the log stream.
+///
+/// It is similar to a FILE stream. It allows a printf() function, and
+/// also to write with a << operator. Moreover, it can prefix
+/// lines with the "PLUMED:" prefix, useful to grep out plumed
+/// log from output
+class Log
+{
+/// Actual FILE stream
+ FILE* fp;
+/// Flag to know if, when Log is destructed, file should be closed
+ bool toBeClosed;
+ static const int buflen=10000;
+ std::ostringstream oss;
+ char* buffer;
+/// Communicator (to write only with the first processor)
+ PlumedCommunicator& comm;
+public:
+/// Initialize on a given communicator
+ Log(PlumedCommunicator&);
+ ~Log();
+/// Set a file with a specific name
+ void setFile(std::string str);
+/// Link to an already open FILE stream
+ void set(FILE*f);
+/// Standard printf-like function
+ int printf(const char*fmt,...);
+ template <class T>
+ friend Log& operator<<(Log&,const T &);
+};
+
+/// Write using << syntax
+template <class T>
+Log& operator<<(Log&log,const T &t){
+ log.oss<<t;
+ log.printf("%s",log.oss.str().c_str());
+ log.oss.str("");
+ return log;
+}
+
+
+}
+
+#endif
diff --git a/src/MDAtoms.cpp b/src/MDAtoms.cpp
new file mode 100644
index 000000000..47a97368f
--- /dev/null
+++ b/src/MDAtoms.cpp
@@ -0,0 +1,243 @@
+#include <cassert>
+#include <algorithm>
+#include <string>
+#include "MDAtoms.h"
+
+using namespace PLMD;
+using namespace std;
+
+namespace PLMD {
+
+template <class T>
+class MDAtomsTyped:
+public MDAtomsBase
+{
+ T *m;
+ T *c;
+ T *px; T *py; T *pz;
+ T *fx; T *fy; T *fz;
+ T *box;
+ T *virial;
+public:
+ MDAtomsTyped();
+ void setm(void*m);
+ void setc(void*m);
+ void setBox(void*);
+ void setp(void*p);
+ void setVirial(void*);
+ void setf(void*f);
+ void setp(void*p,int i);
+ void setf(void*f,int i);
+ void MD2double(const void*m,double&d)const{
+ d=double(*(static_cast<const T*>(m)));
+ }
+ void double2MD(const double&d,void*m)const{
+ *(static_cast<T*>(m))=T(d);
+ }
+ void getBox(Tensor &)const;
+ void getPositions(int first,int last,vector<Vector>&)const;
+ void getPositions(const vector<int>&index,vector<Vector>&positions)const;
+ void getMasses(int first,int last,vector<double>&)const;
+ void getMasses(const vector<int>&index,vector<double>&)const;
+ void getCharges(int first,int last,vector<double>&)const;
+ void getCharges(const vector<int>&index,vector<double>&)const;
+ void updateVirial(const Tensor&)const;
+ void updateForces(int first,int last,const vector<Vector>&);
+ void updateForces(const vector<int>&index,const vector<Vector>&);
+ void rescaleForces(int first,int last,double factor);
+ int getRealPrecision()const;
+};
+
+
+MDAtomsBase::MDAtomsBase():
+ scalep(1.0),
+ scalef(1.0),
+ scaleb(1.0),
+ scalev(1.0),
+ stride(0)
+{
+}
+
+MDAtomsBase* MDAtomsBase::create(int p){
+ if(p==sizeof(double)){
+ return new MDAtomsTyped<double>;
+ } else if (p==sizeof(float)){
+ return new MDAtomsTyped<float>;
+ }
+ assert(0);
+ return NULL;
+}
+
+
+void MDAtomsBase::setUnits(double l,double e){
+ scalep=1.0/l;
+ scalef=e/l;
+ scaleb=1.0/l;
+ scalev=e;
+}
+
+template <class T>
+void MDAtomsTyped<T>::getPositions(int first,int last,vector<Vector>&positions)const{
+ for(int i=first;i<last;i++){
+ positions[i][0]=px[stride*i]*scalep;
+ positions[i][1]=py[stride*i]*scalep;
+ positions[i][2]=pz[stride*i]*scalep;
+ }
+}
+
+template <class T>
+void MDAtomsTyped<T>::getMasses(int first,int last,vector<double>&masses)const{
+ if(m) for(int i=first;i<last;i++) masses[i]=m[i];
+ else for(int i=first;i<last;i++) masses[i]=0.0;
+}
+
+template <class T>
+void MDAtomsTyped<T>::getCharges(int first,int last,vector<double>&charges)const{
+ if(c) for(int i=first;i<last;i++) charges[i]=c[i];
+ else for(int i=first;i<last;i++) charges[i]=0.0;
+}
+
+
+template <class T>
+void MDAtomsTyped<T>::getBox(Tensor&box)const{
+ if(this->box) for(int i=0;i<3;i++)for(int j=0;j<3;j++) box(i,j)=this->box[3*i+j]*scaleb;
+ else box.clear();
+}
+
+template <class T>
+void MDAtomsTyped<T>::getPositions(const vector<int>&index,vector<Vector>&positions)const{
+ for(unsigned i=0;i<index.size();++i){
+ positions[index[i]][0]=px[stride*i]*scalep;
+ positions[index[i]][1]=py[stride*i]*scalep;
+ positions[index[i]][2]=pz[stride*i]*scalep;
+ }
+}
+
+template <class T>
+void MDAtomsTyped<T>::getMasses(const vector<int>&index,vector<double>&masses)const{
+ if(m) for(unsigned i=0;i<index.size();++i) masses[index[i]]=m[i];
+ else for(unsigned i=0;i<index.size();++i) masses[index[i]]=0.0;
+}
+
+template <class T>
+void MDAtomsTyped<T>::getCharges(const vector<int>&index,vector<double>&charges)const{
+ if(c) for(unsigned i=0;i<index.size();++i) charges[index[i]]=c[i];
+ else for(unsigned i=0;i<index.size();++i) charges[index[i]]=0.0;
+}
+
+template <class T>
+void MDAtomsTyped<T>::updateVirial(const Tensor&virial)const{
+ if(this->virial) for(int i=0;i<3;i++)for(int j=0;j<3;j++) this->virial[3*i+j]+=T(virial(i,j)*scalev);
+}
+
+
+template <class T>
+void MDAtomsTyped<T>::updateForces(int first,int last,const vector<Vector>&forces){
+ for(int i=first;i<last;i++){
+ fx[stride*i]+=T(scalef*forces[i][0]);
+ fy[stride*i]+=T(scalef*forces[i][1]);
+ fz[stride*i]+=T(scalef*forces[i][2]);
+ }
+}
+
+template <class T>
+void MDAtomsTyped<T>::updateForces(const vector<int>&index,const vector<Vector>&forces){
+ for(unsigned i=0;i<index.size();++i){
+ fx[stride*i]+=T(scalef*forces[index[i]][0]);
+ fy[stride*i]+=T(scalef*forces[index[i]][1]);
+ fz[stride*i]+=T(scalef*forces[index[i]][2]);
+ }
+}
+
+template <class T>
+void MDAtomsTyped<T>::rescaleForces(int first,int last,double factor){
+ for(int i=first;i<last;++i){
+ fx[stride*i]*=T(factor);
+ fy[stride*i]*=T(factor);
+ fz[stride*i]*=T(factor);
+ }
+}
+
+template <class T>
+int MDAtomsTyped<T>::getRealPrecision()const{
+ return sizeof(T);
+}
+
+template <class T>
+void MDAtomsTyped<T>::setp(void*pp){
+ T*p=static_cast<T*>(pp);
+ assert(stride==0 || stride==3);
+ px=p;
+ py=p+1;
+ pz=p+2;
+ stride=3;
+}
+
+template <class T>
+void MDAtomsTyped<T>::setBox(void*pp){
+ box=static_cast<T*>(pp);
+}
+
+
+template <class T>
+void MDAtomsTyped<T>::setf(void*ff){
+ T*f=static_cast<T*>(ff);
+ assert(stride==0 || stride==3);
+ fx=f;
+ fy=f+1;
+ fz=f+2;
+ stride=3;
+}
+
+template <class T>
+void MDAtomsTyped<T>::setp(void*pp,int i){
+ T*p=static_cast<T*>(pp);
+ assert(stride==0 || stride==1);
+ if(i==0)px=p;
+ if(i==1)py=p;
+ if(i==2)pz=p;
+ stride=1;
+}
+
+template <class T>
+void MDAtomsTyped<T>::setVirial(void*pp){
+ virial=static_cast<T*>(pp);
+}
+
+
+template <class T>
+void MDAtomsTyped<T>::setf(void*ff,int i){
+ T*f=static_cast<T*>(ff);
+ assert(stride==0 || stride==1);
+ if(i==0)fx=f;
+ if(i==1)fy=f;
+ if(i==2)fz=f;
+ stride=1;
+}
+
+template <class T>
+void MDAtomsTyped<T>::setm(void*m){
+ this->m=static_cast<T*>(m);
+}
+
+template <class T>
+void MDAtomsTyped<T>::setc(void*c){
+ this->c=static_cast<T*>(c);
+}
+
+template <class T>
+MDAtomsTyped<T>::MDAtomsTyped():
+ m(NULL),
+ c(NULL),
+ px(NULL),
+ py(NULL),
+ pz(NULL),
+ fx(NULL),
+ fy(NULL),
+ fz(NULL),
+ box(NULL),
+ virial(NULL)
+{}
+
+}
+
diff --git a/src/MDAtoms.h b/src/MDAtoms.h
new file mode 100644
index 000000000..f0cfca73b
--- /dev/null
+++ b/src/MDAtoms.h
@@ -0,0 +1,44 @@
+#ifndef __PLUMED_MDAtoms_h
+#define __PLUMED_MDAtoms_h
+
+#include "Tensor.h"
+#include "Vector.h"
+#include <vector>
+
+namespace PLMD {
+
+class MDAtomsBase
+{
+protected:
+ double scalep,scalef;
+ double scaleb,scalev;
+ int stride;
+public:
+ MDAtomsBase();
+ virtual ~MDAtomsBase(){};
+ virtual void setm(void*m)=0;
+ virtual void setc(void*m)=0;
+ virtual void setBox(void*)=0;
+ virtual void setp(void*p)=0;
+ virtual void setVirial(void*)=0;
+ virtual void setf(void*f)=0;
+ virtual void setp(void*p,int i)=0;
+ virtual void setf(void*f,int i)=0;
+ void setUnits(double,double);
+ virtual void MD2double(const void*,double&)const=0;
+ virtual void double2MD(const double&,void*)const=0;
+ virtual void getBox(Tensor &)const=0;
+ virtual void getPositions(const std::vector<int>&index,std::vector<Vector>&)const=0;
+ virtual void getMasses(const std::vector<int>&index,std::vector<double>&)const=0;
+ virtual void getCharges(const std::vector<int>&index,std::vector<double>&)const=0;
+ virtual void updateVirial(const Tensor&)const=0;
+ virtual void updateForces(const std::vector<int>&index,const std::vector<Vector>&)=0;
+ virtual void rescaleForces(int first,int last,double factor)=0;
+ virtual int getRealPrecision()const=0;
+ static MDAtomsBase* create(int);
+};
+
+}
+
+
+#endif
diff --git a/src/Makefile b/src/Makefile
new file mode 100644
index 000000000..de364d883
--- /dev/null
+++ b/src/Makefile
@@ -0,0 +1,85 @@
+
+-include ../Makefile.conf
+-include ../imd/Makefile.conf
+
+ifndef srcdir
+srcdir=.
+endif
+
+SRC_KERNEL=$(subst $(srcdir)/PlumedStatic.cpp,,$(wildcard $(srcdir)/*.cpp))
+OBJ_KERNEL=$(subst $(srcdir)/,,$(SRC_KERNEL:.cpp=.o))
+
+SRC_WRAPPER=$(srcdir)/PlumedStatic.cpp
+OBJ_WRAPPER=PlumedStatic.o
+
+SRC_DYNAMIC_WRAPPER=$(srcdir)/Plumed.c
+OBJ_DYNAMIC_WRAPPER=Plumed.o
+
+ALL_SRC=$(SRC_KERNEL) $(SRC_WRAPPER) $(SRC_DYNAMIC_WRAPPER)
+
+.PHONY: all clean
+
+ifdef GCCDEP
+all: libplumedKernel.$(SOEXT) libplumed.$(SOEXT) Plumed.o Plumed.inc Plumed.inc.runtime Plumed.inc.shared Plumed.inc.static
+else
+all:
+ @echo No configuration available
+ @echo First run ./configure.sh in the root directory
+endif
+
+PlumedConfig.h: PlumedConfig.h.in
+ sed "s/@SOEXT@/$(SOEXT)/g" $< > $@
+
+check:
+ echo $(OBJ_KERNEL) $(SRC_KERNEL)
+
+libplumedKernel.$(SOEXT): $(OBJ_KERNEL)
+ $(LDSO) -o $@ $^ $(DYNAMIC_LIBS)
+
+libplumed.$(SOEXT): $(OBJ_KERNEL) $(OBJ_WRAPPER)
+ $(LDSO) -o $@ $^ $(DYNAMIC_LIBS)
+
+clean:
+ rm -f *.o
+ rm -f makefile.dep
+ rm -f PlumedConfig.h
+ rm -f Plumed.inc*
+ rm -f *~
+ifdef SOEXT
+ rm -f *.$(SOEXT)
+endif
+
+Plumed.inc: $(OBJ_KERNEL) $(OBJ_WRAPPER) libplumed.$(SOEXT) Plumed.o
+ echo "PLUMED_OBJ=" $(realpath $(OBJ_KERNEL)) $(realpath $(OBJ_WRAPPER)) | sed 's/ / \\\n /g' > $@
+ echo "PLUMED_SHARED_OBJ=" $(realpath libplumed.$(SOEXT)) >> $@
+ echo "PLUMED_WRAPPER=" $(realpath Plumed.o) >> $@
+ echo "PLUMED_INCLUDE="-I$(realpath ../include) >> $@
+ echo "PLUMED_LIBS="$(LIBS) >> $@
+ echo "PLUMED_DYNAMIC_LIBS="$(DYNAMIC_LIBS) >> $@
+ echo "PLUMED_LDFLAGS="$(LDFLAGS) >> $@
+
+Plumed.inc.runtime: Plumed.inc
+ echo "# PLUMED: runtime installation" > $@
+ cat $< >> $@
+ echo PLUMED_LOAD= '$$(PLUMED_WRAPPER) $$(PLUMED_LIBS) $$(PLUMED_LDFLAGS)' >> $@
+ echo PLUMED_DEPENDENCIES= >> $@
+
+Plumed.inc.static: Plumed.inc
+ echo "# PLUMED: static installation" > $@
+ cat $< >> $@
+ echo PLUMED_LOAD= '$$(PLUMED_OBJ) $$(PLUMED_LIBS) $$(PLUMED_DYNAMIC_LIBS) $$(PLUMED_LDFLAGS)' >> $@
+ echo PLUMED_DEPENDENCIES='$$(PLUMED_OBJ)' >> $@
+
+Plumed.inc.shared: Plumed.inc
+ echo "# PLUMED: shared installation" > $@
+ cat $< >> $@
+ echo PLUMED_LOAD= '$$(PLUMED_SHARED_OBJ) $$(PLUMED_LIBS) $$(PLUMED_LDFLAGS)' >> $@
+ echo PLUMED_DEPENDENCIES='$$(PLUMED_SHARED_OBJ)' >> $@
+
+makefile.dep : $(ALL_SRC) $(srcdir)/*.h $(srcdir)/PlumedConfig.h
+ifdef GCCDEP
+ for i in $(ALL_SRC) ; do $(GCCDEP) $(CPPFLAGS) -MM "$${i}"; done > $@
+endif
+
+-include makefile.dep
+
diff --git a/src/Pbc.cpp b/src/Pbc.cpp
new file mode 100644
index 000000000..42e81aca3
--- /dev/null
+++ b/src/Pbc.cpp
@@ -0,0 +1,66 @@
+#include "Pbc.h"
+#include "Tools.h"
+
+using namespace PLMD;
+
+Pbc::Pbc():
+ type(unset)
+{
+ box.clear();
+ invBox.clear();
+}
+
+
+void Pbc::setBox(const Tensor&b){
+ box=b;
+// UP TO NOW ONLY WORKS WITH ORTHOROMIBIC (should implement matrix inversion)
+// detect type:
+ const double epsilon=1e-14;
+ bool cxy=false;
+ bool cxz=false;
+ bool cyz=false;
+ if(box(0,1)*box(0,1)<epsilon && box(1,0)*box(1,0)<epsilon) cxy=true;
+ if(box(0,2)*box(0,2)<epsilon && box(2,0)*box(2,0)<epsilon) cxz=true;
+ if(box(1,2)*box(1,2)<epsilon && box(2,1)*box(2,1)<epsilon) cyz=true;
+
+ invBox=box.inverse();
+
+ if(cxy && cxz && cyz) type=orthorombic;
+// NOT IMPLEMENTED YET; WILL FALL TO GENERIC
+// else if(cxy && cxz) type=yz;
+// else if(cxy && cyz) type=xz;
+// else if(cxz && cyz) type=xy;
+ else type=generic;
+}
+
+Vector Pbc::distance(const Vector&v1,const Vector&v2)const{
+ Vector d=delta(v1,v2);
+ if(type==unset){
+ } else if(type==orthorombic) {
+ for(int i=0;i<3;i++) d[i]=Tools::pbc(d[i]*invBox(i,i))*box(i,i);
+ } else if(type==generic) {
+// first reduce:
+ Vector s=matmul(invBox.transpose(),d);
+ for(int i=0;i<3;i++) s[i]=Tools::pbc(s[i]);
+ d=matmul(box.transpose(),s);
+// then check all the neighbors:
+ Vector a1(box(0,0),box(0,1),box(0,2));
+ Vector a2(box(1,0),box(1,1),box(1,2));
+ Vector a3(box(2,0),box(2,1),box(2,2));
+ Vector best(d);
+ double lbest=best.modulo2();
+ Vector trial;
+ double ltrial;
+ for(int i=-1;i<=1;i++) for(int j=-1;j<=1;j++) for(int k=-1;k<=1;k++) {
+ trial=d+i*a1+j*a2+k*a3;
+ ltrial=trial.modulo2();
+ if(ltrial<lbest){
+ best=trial;
+ lbest=ltrial;
+ }
+ }
+ d=best;
+ } else assert(0);
+ return d;
+}
+
diff --git a/src/Pbc.h b/src/Pbc.h
new file mode 100644
index 000000000..244521c78
--- /dev/null
+++ b/src/Pbc.h
@@ -0,0 +1,21 @@
+#ifndef __PLUMED_Pbc_h
+#define __PLUMED_Pbc_h
+#include <cassert>
+#include "Vector.h"
+#include "Tensor.h"
+
+namespace PLMD{
+
+class Pbc{
+ enum {unset,orthorombic,xy,xz,yz,generic} type;
+ Tensor box;
+ Tensor invBox;
+public:
+ Pbc();
+ Vector distance(const Vector&,const Vector&)const;
+ void setBox(const Tensor&);
+};
+
+}
+
+#endif
diff --git a/src/Plumed.c b/src/Plumed.c
new file mode 100644
index 000000000..d697e7af8
--- /dev/null
+++ b/src/Plumed.c
@@ -0,0 +1,194 @@
+#ifdef __PLUMED_HAS_DLOPEN
+#include <dlfcn.h>
+#endif
+
+#include "Plumed.h"
+#include <stdio.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+
+/* DECLARATION USED ONLY IN THIS FILE */
+
+#ifdef __cplusplus
+ extern "C" {
+#endif
+
+/**
+ Holder for plumedmain function pointers.
+*/
+typedef struct {
+ void*(*create)(void);
+ void(*cmd)(void*,const char*,const void*);
+ void(*finalize)(void*);
+} plumed_plumedmain_function_holder;
+
+/**
+ Register for plumedmain function pointers
+*/
+plumed_plumedmain_function_holder* plumed_kernel_register(const plumed_plumedmain_function_holder*);
+
+/**
+ Routine to load a shared library
+*/
+void* plumed_dlopen(const char*);
+
+#ifdef __PLUMED_STATIC_KERNEL
+/* Real interface */
+void*plumedmain_create(void);
+void plumedmain_cmd(void*,const char*,const void*);
+void plumedmain_finalize(void*);
+#else
+/* dummy interface */
+void*plumed_dummy_create(void);
+void plumed_dummy_cmd(void*,const char*,const void*);
+void plumed_dummy_finalize(void*);
+#endif
+
+#ifdef __cplusplus
+ }
+#endif
+
+/* END OF DECLARATION USED ONLY IN THIS FILE */
+
+
+/*
+ this routine can be adjusted for different systems
+ it should try to load the shared object indicated in the path
+*/
+
+void* plumed_dlopen(const char* path){
+#ifdef __PLUMED_HAS_DLOPEN
+ return dlopen(path,RTLD_NOW|RTLD_GLOBAL);
+#else
+ return NULL;
+#endif
+}
+
+
+/* These are the dummy routines which are used when plumed is not available */
+
+#ifdef __PLUMED_STATIC_KERNEL
+
+static int installed=1;
+
+#else
+
+static int installed=0;
+
+static int dummy;
+
+void*plumed_dummy_create(void){
+ return (void*)&dummy;
+}
+
+void plumed_dummy_cmd(void*p,const char*key,const void*val){
+ (void) p; /* avoid warning on unused parameter */
+ (void) key; /* avoid warning on unused parameter */
+ (void) val; /* avoid warning on unused parameter */
+ fprintf(stderr,"+++ ERROR +++");
+ fprintf(stderr,"YOU ARE TRYING TO USE PLUMED, BUT IT IS NOT AVAILABLE\n");
+ exit(1);
+}
+
+void plumed_dummy_finalize(void*p){
+ (void) p; /* avoid warning on unused parameter */
+}
+
+#endif
+
+plumed_plumedmain_function_holder* plumed_kernel_register(const plumed_plumedmain_function_holder* f){
+#ifdef __PLUMED_STATIC_KERNEL
+ static plumed_plumedmain_function_holder g={plumedmain_create,plumedmain_cmd,plumedmain_finalize};
+ (void) f; /* avoid warning on unused parameter */
+ return &g;
+#else
+ static plumed_plumedmain_function_holder g={plumed_dummy_create,plumed_dummy_cmd,plumed_dummy_finalize};
+ static int first=1;
+#ifdef __PLUMED_HAS_DLOPEN
+ char* path;
+ void* p;
+#endif
+ if(first && f==NULL){
+#ifdef __PLUMED_HAS_DLOPEN
+ path=getenv("PLUMED_KERNEL");
+ if(path && (*path)){
+ fprintf(stderr,"+++ PLUMED kernel is being loaded as \"%s\" ...",path);
+ p=plumed_dlopen(path);
+ if(p){
+ fprintf(stderr,"ok\n");
+ installed=1;
+ }
+ else fprintf(stderr,"NOT FOUND !!!\n");
+ }
+#endif
+ }
+ first=0;
+ if(f) g=*f;
+ return &g;
+#endif
+}
+
+/* C wrappers: */
+
+plumed plumed_create(void){
+ plumed p;
+ p.p=(*(plumed_kernel_register(NULL)->create))();
+ return p;
+}
+
+void plumed_cmd(plumed p,const char*key,const void*val){
+ (*(plumed_kernel_register(NULL)->cmd))(p.p,key,val);
+}
+
+void plumed_finalize(plumed p){
+ (*(plumed_kernel_register(NULL)->finalize))(p.p);
+}
+
+void plumed_installed(int*i){
+ plumed_kernel_register(NULL);
+ *i=installed;
+}
+
+/* we declare a Plumed_g_main object here, in such a way that it is always available */
+
+static plumed plumed_g_main={NULL};
+
+void plumed_g_create(void){
+ plumed_g_main.p=(*(plumed_kernel_register(NULL)->create))();
+}
+
+void plumed_g_cmd(const char*key,const void*val){
+ assert(plumed_g_main.p);
+ (*(plumed_kernel_register(NULL)->cmd))(plumed_g_main.p,key,val);
+}
+
+void plumed_g_finalize(void){
+ assert(plumed_g_main.p);
+ (*(plumed_kernel_register(NULL)->finalize))(plumed_g_main.p);
+ plumed_g_main.p=NULL;
+}
+
+/* Fortran wrappers */
+/* These are just like the global C wrappers, with an added underscore */
+
+void plumed_g_create_(void){
+ plumed_g_main.p=(*(plumed_kernel_register(NULL)->create))();
+}
+
+void plumed_g_cmd_(const char* key,const void* val){
+ assert(plumed_g_main.p);
+ (*(plumed_kernel_register(NULL)->cmd))(plumed_g_main.p,key,val);
+}
+
+void plumed_g_finalize_(void){
+ assert(plumed_g_main.p);
+ (*(plumed_kernel_register(NULL)->finalize))(plumed_g_main.p);
+ plumed_g_main.p=NULL;
+}
+
+void plumed_installed_(int*i){
+ plumed_kernel_register(NULL);
+ *i=installed;
+}
+
diff --git a/src/Plumed.h b/src/Plumed.h
new file mode 100644
index 000000000..c6f041b6f
--- /dev/null
+++ b/src/Plumed.h
@@ -0,0 +1,238 @@
+#ifndef __PLUMED_Plumed_h
+#define __PLUMED_Plumed_h
+
+/*
+ Plumed.h and Plumed.c contain the external plumed interface, which is used to
+ integrate it with MD engines. This interface is very general, and is expected
+ not to change across plumed versions. Plumed.c also implements a dummy version
+ of the interface. These files could be directly included in the official
+ host MD distribution. In this manner, it will be sufficient to link the plumed
+ library at link time (on all systems) or directly at runtime (on some system)
+ to include plumed features.
+ The C++ interface is more or less equivalent to the PlumedMain class, but it is
+ based on the plumed_{create,cmd,finalize} C interface. In this manner it
+ can take advantage of dynamic binding.
+
+ The available actions are:
+ create --- creates a plumed object (in C++ this is done by the constructor)
+ cmd --- sends a command to the plumed object
+ finalize --- destroys a plumed object (in C++ this is done by the destructor)
+
+ The dummy interface does:
+ create --- don't do anything
+ cmd --- report an error and die
+ finalize --- don't do anything
+
+ There is also a "global" interface, where a static plumed object is used. It can be called
+ also from FORTRAN.
+
+ C++ interface:
+ bool installed();
+ class PLMD::Plumed{
+ cmd(const char* key,const void* val=NULL);
+ }
+ C interface (can be used in C/C++)
+ void plumed_installed(int*)
+ struct plumed;
+ plumed plumed_create();
+ void plumed_cmd(plumed p,const char* key,const void* val);
+ void plumed_finalize(plumed p);
+ Global interface (can be used in C/C++/FORTRAN)
+ plumed_installed(int*)
+ plumed_g_create();
+ plumed_g_command(const char* key,const void* val);
+ plumed_g_finalize();
+
+ The main routine is "cmd", which accepts two arguments:
+ key is a string containing the name of the command
+ val is the argument. it is declared const so as to use allow passing const objects, but in practice plumed
+ is going to modify val in several cases (using a const_cast).
+ In some cases val can be omitted: just pass a NULL pointer (in C++, val is optional and can be omitted).
+ The set of possible keys is the real API of the plumed library, and will be expanded with time.
+ New commands will be added, but backward compatibility will be retained as long as possible.
+
+ The plumed_install routine set its argument to a positive integer if plumed is installed,
+ to zero otherwise. Similarly, the C++ version installed() returns true in the first case and
+ false in the second. This is useful for the host MD code to know if
+ plumed has been linked or not, and is the only command which can be executed in the dummy interface.
+
+ To pass plumed a callback function use the following syntax:
+ plumed_function_holder ff;
+ ff.p=your_function;
+ plumed_cmd(plumed,"xxxx",&ff);
+ (this is passing the your_function() function to the "xxxx" command)
+*/
+
+#ifdef __cplusplus
+ extern "C" {
+#endif
+
+/**
+ \brief Main plumed object
+
+ This is an object containing a Plumed instance, which should be used in
+ the MD engine. It should first be initialized with plumed_create(),
+ then it communicates with the MD engine using plumed_cmd(). Finally,
+ before the termination, it should be deallocated with plumed_finalize().
+ Its interface is very simple and general, and is expected
+ not to change across plumed versions.
+*/
+typedef struct {
+/**
+ \private
+ \brief Void pointer holding the real PlumedMain structure
+*/
+ void*p;
+} plumed;
+
+/* Generic function pointer */
+typedef void (*plumed_function_pointer)(void);
+
+/**
+ \brief Holder for function pointer.
+
+ To pass plumed a callback function use the following syntax:
+
+ plumed_function_holder ff;
+
+ ff.p=your_function;
+
+ plumed_cmd(plumed,"xxxx",&ff);
+
+ (this is passing the your_function() function to the "xxxx" command)
+*/
+
+typedef struct {
+ plumed_function_pointer p;
+} plumed_function_holder;
+
+/* C interface: */
+
+/** \relates plumed
+ \brief Constructor
+
+ \return The constructed plumed object
+*/
+plumed plumed_create(void);
+
+/** \relates plumed
+ \brief Tells p to execute a command
+
+ \param p The plumed object on which command is acting
+ \param key The name of the command to be executed
+ \param val The argument. It is declared as const to allow calls like plumed_cmd("A","B"),
+ but for some choice of key it can change the content
+*/
+void plumed_cmd(plumed p,const char*key,const void*val);
+
+/** \relates plumed
+ \brief Destructor
+
+ \param p The plumed object to be deallocated
+*/
+void plumed_finalize(plumed p);
+
+/** \relates plumed
+ \brief Check if plumed is installed (for runtime binding)
+
+ \param flag Is set to 1 if plumed is installed, to 0 otherwise
+*/
+void plumed_installed(int*flag);
+
+/* global C interface, working on a global object */
+
+/** \relates plumed
+ \brief Constructor for the global interface.
+
+ Equivalent to plumed_create(), but initialize a static global plumed object
+*/
+void plumed_g_create(void);
+
+/** \relates plumed
+ \brief Tells to the global interface to execute a command.
+
+ Equivalent to plumed_cmd(), but skipping the plumed argument
+*/
+void plumed_g_cmd(const char*,const void*);
+
+/** \relates plumed
+ \brief Destructor for the global interface.
+
+ Equivalent to plumed_finalize(), but skipping the plumed argument
+*/
+void plumed_g_finalize(void);
+
+/* fortran (underscored) wrappers, only to the global interface */
+
+
+/** \relates plumed
+ \brief Same as plumed_g_create().
+
+*/
+void plumed_g_create_(void);
+
+/** \relates plumed
+ \brief Same as plumed_g_cmd().
+
+*/
+
+void plumed_g_cmd_(const char*,const void*);
+/** \relates plumed
+ \brief Same as plumed_g_finalize().
+
+*/
+void plumed_g_finalize_(void);
+
+/** \relates plumed
+ \brief Same as plumed_installed().
+
+*/
+void plumed_installed_(int*);
+
+#ifdef __cplusplus
+ }
+#endif
+
+#ifdef __cplusplus
+
+/* this is to include the NULL pointer */
+#include <cstdlib>
+
+/* C++ interface is hidden in PLMD namespace (same as plumed library) */
+namespace PLMD {
+
+/**
+ C++ wrapper for \link plumed
+*/
+
+class Plumed{
+ plumed main;
+public:
+/**
+ Constructor - equivalent to plumed_create()
+*/
+ Plumed(){main=plumed_create();};
+/**
+ Cmd - equivalent to plumed_cmd()
+*/
+ void cmd(const char*key,const void*val=NULL){plumed_cmd(main,key,val);};
+/**
+ Destructor - equivalent to plumed_finalize()
+*/
+ ~Plumed(){plumed_finalize(main);};
+};
+
+/** \relates Plumed
+ \brief Check if plumed is installed (for runtime binding)
+
+ \return true if plumed is installed, false otherwise
+*/
+inline
+bool installed(){int i;plumed_installed(&i);if(i>0) return true;else return false;}
+
+}
+
+#endif
+
+
+#endif
diff --git a/src/PlumedCommunicator.cpp b/src/PlumedCommunicator.cpp
new file mode 100644
index 000000000..be103f60b
--- /dev/null
+++ b/src/PlumedCommunicator.cpp
@@ -0,0 +1,119 @@
+#include "PlumedCommunicator.h"
+#include <cstdlib>
+#include <cassert>
+
+using namespace std;
+using namespace PLMD;
+
+namespace PLMD{
+
+PlumedCommunicator::PlumedCommunicator()
+#ifdef __PLUMED_MPI
+: communicator(MPI_COMM_SELF)
+#endif
+{
+}
+
+int PlumedCommunicator::Get_rank()const{
+ int r=0;
+#ifdef __PLUMED_MPI
+ if(initialized()) MPI_Comm_rank(communicator,&r);
+#endif
+ return r;
+}
+
+int PlumedCommunicator::Get_size()const{
+ int s=1;
+#ifdef __PLUMED_MPI
+ if(initialized()) MPI_Comm_size(communicator,&s);
+#endif
+ return s;
+}
+
+void PlumedCommunicator::Set_comm(MPI_Comm c){
+#ifdef __PLUMED_MPI
+ if(initialized()){
+ if(communicator!=MPI_COMM_SELF) MPI_Comm_free(&communicator);
+ if(c!=MPI_COMM_SELF) MPI_Comm_dup(c,&communicator);
+ }
+#else
+ (void) c;
+#endif
+}
+
+PlumedCommunicator::~PlumedCommunicator(){
+#ifdef __PLUMED_MPI
+ if(initialized() && communicator!=MPI_COMM_SELF) MPI_Comm_free(&communicator);
+#endif
+}
+
+void PlumedCommunicator::Set_comm(void*val){
+#ifdef __PLUMED_MPI
+ if(initialized()&&val) Set_comm(*(MPI_Comm*)val);
+#else
+ (void) val;
+ assert(0);
+#endif
+}
+
+void PlumedCommunicator::Set_fcomm(void*val){
+#ifdef __PLUMED_MPI
+ if(initialized() && val){
+ MPI_Comm comm=MPI_Comm_f2c(*(MPI_Fint*)val);
+ Set_comm(comm);
+ }
+#else
+ (void) val;
+ assert(0);
+#endif
+}
+
+void PlumedCommunicator::Abort(int errorcode){
+#ifdef __PLUMED_MPI
+ if(initialized()){
+ MPI_Abort(communicator,errorcode);
+ }
+ std::exit(errorcode);
+#else
+ std::exit(errorcode);
+#endif
+}
+
+MPI_Comm & PlumedCommunicator::Get_comm(){
+ return communicator;
+}
+
+bool PlumedCommunicator::initialized(){
+ int flag=false;
+#if defined(__PLUMED_MPI)
+ MPI_Initialized(&flag);
+#endif
+ if(flag) return true;
+ else return false;
+}
+
+void PlumedCommunicator::Request::wait(){
+#ifdef __PLUMED_MPI
+ if(initialized())MPI_Wait(&r,MPI_STATUS_IGNORE);
+#else
+ assert(0);
+#endif
+}
+
+void PlumedCommunicator::Request::wait(Status&s){
+#ifdef __PLUMED_MPI
+ if(initialized()) MPI_Wait(&r,&s.s);
+#else
+ (void) s;
+ assert(0);
+#endif
+}
+
+#ifdef __PLUMED_MPI
+template<> MPI_Datatype PlumedCommunicator::getMPIType<float>(){ return MPI_FLOAT;}
+template<> MPI_Datatype PlumedCommunicator::getMPIType<double>(){ return MPI_DOUBLE;}
+template<> MPI_Datatype PlumedCommunicator::getMPIType<int>() { return MPI_INT;}
+#endif
+
+}
+
diff --git a/src/PlumedCommunicator.h b/src/PlumedCommunicator.h
new file mode 100644
index 000000000..555ff2479
--- /dev/null
+++ b/src/PlumedCommunicator.h
@@ -0,0 +1,184 @@
+#ifndef __PLUMED_PlumedCommunicator_h
+#define __PLUMED_PlumedCommunicator_h
+#ifdef __PLUMED_MPI
+#include <mpi.h>
+#endif
+#include <cstdlib>
+#include <cassert>
+
+namespace PLMD{
+
+#ifndef __PLUMED_MPI
+/// Surrogate of MPI types when MPI library is not available
+ class MPI_Comm {
+ int dummy;
+ };
+#endif
+
+/// Class containing wrappers to MPI.
+/// All the MPI related stuff is relegated here.
+class PlumedCommunicator{
+/// Communicator
+ MPI_Comm communicator;
+#ifdef __PLUMED_MPI
+ template <class T>
+ static MPI_Datatype getMPIType();
+#endif
+public:
+ class Status{
+ public:
+#ifdef __PLUMED_MPI
+ MPI_Status s;
+#endif
+ template <class T>
+ int Get_count()const;
+ };
+ class Request{
+ public:
+#ifdef __PLUMED_MPI
+ MPI_Request r;
+#endif
+ void wait();
+ void wait(Status&);
+ };
+ PlumedCommunicator();
+ virtual ~PlumedCommunicator();
+/// Obtain the rank of the present process
+ int Get_rank()const;
+/// Obtain the number of processes
+ int Get_size()const;
+/// Set from a real MPI communicator
+ void Set_comm(MPI_Comm);
+/// Reference to MPI communicator
+ MPI_Comm & Get_comm();
+/// Set from a pointer to a real MPI communicator (C)
+/// \param comm Pointer to a C MPI communicator
+ void Set_comm(void*comm);
+/// Set from a pointer to a real MPI communicator (FORTRAN)
+/// \param comm Pointer to a FORTRAN MPI communicator (INTEGER)
+ void Set_fcomm(void*comm);
+/// Wrapper to MPI_Abort
+ void Abort(int);
+
+/// Tests if MPI library is initialized
+ static bool initialized();
+
+/// Wrapper for MPI_Allreduce with MPI_SUM
+ template <class T>
+ void Sum(T*,int);
+/// Wrapper for MPI_Allgatherv
+ template <class T>
+ void Allgatherv(const T*,int,T*,const int*,const int*);
+ template <class T>
+ Request Isend(T*,int,int,int);
+ template <class T>
+ void Recv(T*,int,int,int,Status&);
+ template <class T>
+ void Recv(T*,int,int,int);
+ template <class T>
+ void Bcast(T*,int,int);
+};
+
+template<class T>
+void PlumedCommunicator::Sum(T*b,int count){
+#if defined(__PLUMED_MPI)
+ if(initialized()) MPI_Allreduce(MPI_IN_PLACE,b,count,getMPIType<T>(),MPI_SUM,communicator);
+#else
+ (void) b;
+ (void) count;
+#endif
+}
+
+template<class T>
+void PlumedCommunicator::Bcast(T*b,int count,int root){
+#if defined(__PLUMED_MPI)
+ if(initialized()) MPI_Bcast(b,count,getMPIType<T>(),root,communicator);
+#else
+ (void) b;
+ (void) count;
+ (void) root;
+#endif
+}
+
+
+template<class T>
+void PlumedCommunicator::Allgatherv(const T*sendbuf,int sendcount,T*recvbuf,const int*recvcounts,const int*displs){
+#if defined(__PLUMED_MPI)
+ if(initialized()){
+ void*s=const_cast<void*>((const void*)sendbuf);
+ void*r=const_cast<void*>((const void*)recvbuf);
+ int*rc=const_cast<int*>(recvcounts);
+ int*di=const_cast<int*>(displs);
+ if(s==NULL)s=MPI_IN_PLACE;
+ MPI_Allgatherv(s,sendcount,getMPIType<T>(),r,rc,di,getMPIType<T>(),communicator);
+ }
+#else
+ (void) sendbuf;
+ (void) sendcount;
+ (void) recvbuf;
+ (void) recvcounts;
+ (void) displs;
+ assert(0);
+#endif
+}
+
+template <class T>
+PlumedCommunicator::Request PlumedCommunicator::Isend(T*buf,int count,int source,int tag){
+ Request req;
+#ifdef __PLUMED_MPI
+ if(initialized())MPI_Isend(buf,count,getMPIType<T>(),source,tag,communicator,&req.r);
+#else
+ (void) buf;
+ (void) count;
+ (void) source;
+ (void) tag;
+ assert(0);
+#endif
+ return req;
+}
+
+template <class T>
+void PlumedCommunicator::Recv(T*buf,int count,int source,int tag,Status&status){
+#ifdef __PLUMED_MPI
+ if(initialized()){
+ MPI_Recv(buf,count,getMPIType<T>(),source,tag,communicator,&status.s);
+ }
+#else
+ (void) buf;
+ (void) count;
+ (void) source;
+ (void) tag;
+ (void) status;
+ assert(0);
+#endif
+}
+
+template <class T>
+void PlumedCommunicator::Recv(T*buf,int count,int source,int tag){
+#ifdef __PLUMED_MPI
+ if(initialized())MPI_Recv(buf,count,getMPIType<T>(),source,tag,communicator,MPI_STATUS_IGNORE);
+#else
+ (void) buf;
+ (void) count;
+ (void) source;
+ (void) tag;
+ assert(0);
+#endif
+}
+
+template<class T>
+int PlumedCommunicator::Status::Get_count()const{
+ int i;
+#ifdef __PLUMED_MPI
+ if(initialized()) MPI_Get_count(const_cast<MPI_Status*>(&s),getMPIType<T>(),&i);
+#else
+ assert(0);
+#endif
+ return i;
+}
+
+
+
+}
+
+#endif
diff --git a/src/PlumedConfig.h.in b/src/PlumedConfig.h.in
new file mode 100644
index 000000000..cd0fede88
--- /dev/null
+++ b/src/PlumedConfig.h.in
@@ -0,0 +1,12 @@
+#ifndef __PLUMED_PlumedConfig_h
+#define __PLUMED_PlumedConfig_h
+
+namespace PLMD{
+
+// nothing yet
+
+const std::string soext("@SOEXT@");
+
+}
+
+#endif
diff --git a/src/PlumedMain.cpp b/src/PlumedMain.cpp
new file mode 100644
index 000000000..21125036a
--- /dev/null
+++ b/src/PlumedMain.cpp
@@ -0,0 +1,442 @@
+#include "PlumedMain.h"
+#include "Tools.h"
+#include <cstring>
+#include <assert.h>
+#include "ActionPilot.h"
+#include "ActionWithValue.h"
+#include "ActionAtomistic.h"
+#include "Atoms.h"
+#include <set>
+#include "PlumedConfig.h"
+#include "Colvar.h"
+
+#include <cstdlib>
+
+#include "ActionRegister.h"
+
+using namespace PLMD;
+
+// !!!!!!!!!!!!!!!!!!!!!! DANGER !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
+// THE FOLLOWING ARE UTILITIES WHICH ARE NECESSARY FOR DYNAMIC LOADING OF THE PLUMED KERNEL:
+// This section should be consistent with the Plumed.h file.
+// Since the Plumed.h file may be included in host MD codes, **NEVER** MODIFY THE CODE DOWN HERE
+
+/* Holder for plumedmain function pointers */
+typedef struct {
+ void*(*create)();
+ void(*cmd)(void*,const char*,const void*);
+ void(*finalize)(void*);
+} plumed_plumedmain_function_holder;
+
+extern "C" void*plumedmain_create();
+extern "C" void plumedmain_cmd(void*plumed,const char*key,const void*val);
+extern "C" void plumedmain_finalize(void*plumed);
+
+void*plumedmain_create(){
+ return new PlumedMain;
+}
+
+void plumedmain_cmd(void*plumed,const char*key,const void*val){
+ assert(plumed);
+ static_cast<PlumedMain*>(plumed)->cmd(key,val);
+}
+
+void plumedmain_finalize(void*plumed){
+ assert(plumed);
+ delete static_cast<PlumedMain*>(plumed);
+}
+
+extern "C" plumed_plumedmain_function_holder* plumed_kernel_register(const plumed_plumedmain_function_holder*);
+extern "C" void* plumed_dlopen(const char*);
+
+namespace PLMD{
+
+/// Static object which registers Plumed.
+/// This is a static object which, during its construction at startup,
+/// registers the pointers to plumedmain_create, plumedmain_cmd and plumedmain_finalize
+/// to the plumed_kernel_register function
+static class PlumedMainInitializer{
+ public:
+ PlumedMainInitializer(){
+ plumed_plumedmain_function_holder fh={plumedmain_create,plumedmain_cmd,plumedmain_finalize};
+ plumed_kernel_register(&fh);
+ };
+} RegisterMe;
+
+}
+
+// END OF DANGER
+////////////////////////////////////////////////////////////
+
+
+PlumedMain::PlumedMain():
+ initialized(false),
+ log(comm),
+ step(0),
+ active(false),
+ actionSet((*this)),
+ atoms(*this),
+ novirial(false)
+{
+}
+
+/////////////////////////////////////////////////////////////
+// MAIN INTERPRETER
+
+void PlumedMain::cmd(const char*key,const void*cval){
+
+// this is nasty trick:
+ void* val=const_cast<void*>(cval);
+// in this manner, a const pointer can be used for cval, allowing the user to pass
+// arguments such as cmd("pippo","pluto")
+// but here we override the const
+
+// first try single word keys
+ std::string word(key);
+
+ if(false){
+// for efficiency, words frequently used are checked first
+
+// words used at every MD steps:
+ } else if(word=="setBox") {
+ assert(initialized);
+ assert(val);
+ atoms.setBox(val);
+ } else if(word=="setPositions") {
+ assert(initialized);
+ assert(val);
+ atoms.setPositions(val);
+ } else if(word=="setMasses") {
+ assert(initialized);
+ assert(val);
+ atoms.setMasses(val);
+ } else if(word=="setCharges") {
+ assert(initialized);
+ assert(val);
+ atoms.setCharges(val);
+ } else if(word=="setPositionsX") {
+ assert(initialized);
+ assert(val);
+ atoms.setPositions(val,0);
+ } else if(word=="setPositionsY") {
+ assert(initialized);
+ assert(val);
+ atoms.setPositions(val,1);
+ } else if(word=="setPositionsZ") {
+ assert(initialized);
+ assert(val);
+ atoms.setPositions(val,2);
+ } else if(word=="setVirial") {
+ assert(initialized);
+ assert(val);
+ atoms.setVirial(val);
+ } else if(word=="setEnergy") {
+ assert(initialized);
+ assert(val);
+ atoms.setEnergy(val);
+ } else if(word=="setForces") {
+ assert(initialized);
+ assert(val);
+ atoms.setForces(val);
+ } else if(word=="setForcesX") {
+ assert(initialized);
+ assert(val);
+ atoms.setForces(val,0);
+ } else if(word=="setForcesY") {
+ assert(initialized);
+ assert(val);
+ atoms.setForces(val,1);
+ } else if(word=="setForcesZ") {
+ assert(initialized);
+ assert(val);
+ atoms.setForces(val,2);
+ } else if(word=="calc") {
+ assert(initialized);
+ calc();
+ } else if(word=="prepareDependencies") {
+ assert(initialized);
+ prepareDependencies();
+ } else if(word=="shareData") {
+ assert(initialized);
+ shareData();
+ } else if(word=="prepareCalc") {
+ assert(initialized);
+ prepareCalc();
+ } else if(word=="performCalc") {
+ assert(initialized);
+ performCalc();
+ } else if(word=="setStep") {
+ assert(initialized);
+ step=(*static_cast<int*>(val));
+// words used less frequently:
+ } else if(word=="setAtomsNlocal"){
+ assert(initialized);
+ assert(val);
+ atoms.setAtomsNlocal(*static_cast<int*>(val));
+ } else if(word=="setAtomsGatindex"){
+ assert(initialized);
+ assert(val);
+ atoms.setAtomsGatindex(static_cast<int*>(val));
+ } else if(word=="setAtomsContiguous"){
+ assert(initialized);
+ assert(val);
+ atoms.setAtomsContiguous(*static_cast<int*>(val));
+ } else if(word=="createFullList"){
+ assert(initialized);
+ atoms.createFullList(static_cast<int*>(val));
+ } else if(word=="getFullList"){
+ assert(initialized);
+ atoms.getFullList(static_cast<int**>(val));
+ } else if(word=="clearFullList"){
+ assert(initialized);
+ atoms.clearFullList();
+ } else if(word=="read"){
+ assert(initialized);
+ if(val)readInputFile(static_cast<char*>(val));
+ else readInputFile("plumed.dat");
+ } else if(word=="clear"){
+ assert(initialized);
+ actionSet.clearDelete();
+ } else if(word=="getApiVersion"){
+ *(static_cast<int*>(val))=1;
+// commands which can be used only before initialization:
+ } else if(word=="init"){
+ assert(!initialized);
+ init();
+ } else if(word=="setRealPrecision"){
+ assert(!initialized);
+ assert(val);
+ atoms.setRealPrecision(*static_cast<int*>(val));
+ } else if(word=="setMDLengthUnits"){
+ assert(!initialized);
+ double d;
+ atoms.MD2double(val,d);
+ atoms.setMDLengthUnits(d);
+ } else if(word=="setMDEnergyUnits"){
+ assert(!initialized);
+ double d;
+ atoms.MD2double(val,d);
+ atoms.setMDEnergyUnits(d);
+ } else if(word=="setMDTimeUnits"){
+ assert(!initialized);
+ double d;
+ atoms.MD2double(val,d);
+ atoms.setMDTimeUnits(d);
+ } else if(word=="setPlumedDat"){
+ assert(!initialized);
+ plumedDat=static_cast<char*>(val);
+ } else if(word=="setMPIComm"){
+ assert(!initialized);
+ comm.Set_comm(val);
+ atoms.setDomainDecomposition(comm);
+ } else if(word=="setMPIFComm"){
+ assert(!initialized);
+ comm.Set_fcomm(val);
+ atoms.setDomainDecomposition(comm);
+ } else if(word=="setNatoms"){
+ assert(!initialized);
+ assert(val);
+ atoms.setNatoms(*static_cast<int*>(val));
+ } else if(word=="setTimestep"){
+ assert(!initialized);
+ assert(val);
+ atoms.setTimeStep(val);
+ } else if(word=="setMDEngine"){
+ assert(!initialized);
+ assert(val);
+ assert(MDEngine.length()==0);
+ MDEngine=static_cast<char*>(val);
+ } else if(word=="setLog"){
+ assert(!initialized);
+ log.set(static_cast<FILE*>(val));
+ } else if(word=="setLogFile"){
+ assert(!initialized);
+ log.setFile(static_cast<char*>(val));
+ } else if(word=="setKBoltzman"){
+ assert(val);
+//
+ } else {
+// multi word commands
+
+ std::vector<std::string> words=Tools::getWords(key);
+ int nw=words.size();
+
+ if(false){
+ } else if(nw==2 && words[0]=="checkAction"){
+ int check=0;
+ if(actionRegister().check(words[1])) check=1;
+ *(static_cast<int*>(val))=check;
+ } else{
+ // error
+ fprintf(stderr,"+++ PLUMED ERROR\n");
+ fprintf(stderr,"+++ CANNOT INTERPRET CALL TO cmd() ROUTINE WITH ARG %s\n",key);
+ fprintf(stderr,"+++ There might be a mistake in the MD code\n");
+ fprintf(stderr,"+++ or you may be using an out-dated plumed version\n");
+ exit(1);
+ };
+ };
+}
+
+/////
+////////////////////////////////////////////////////////////////////////
+
+void PlumedMain::init(){
+// check that initialization just happens once
+ initialized=true;
+ atoms.init();
+ log<<"PLUMED is starting\n";
+ log<<"**** THIS IS AN EXPERIMENTAL VERSION ****\n";
+ log<<"PLUMED compiled on " __DATE__ " at " __TIME__ "\n";
+ log.printf("Please read and cite:\n");
+ log.printf(" M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri,\n");
+ log.printf(" D. Donadio, F. Marinelli, F. Pietrucci, R. A. Broglia and M. Parrinello\n");
+ log.printf(" PLUMED: a portable plugin for free-energy calculations with molecular dynamics\n");
+ log.printf(" Comp. Phys. Comm. 180, 1961 (2009)\n");
+ log.printf("For further information see the PLUMED web page at merlino.mi.infn.it/~plumed\n");
+ log.printf("List of registered actions:\n");
+ actionRegister().log(log);
+ log.printf("Molecular dynamics engine: %s\n",MDEngine.c_str());
+ log.printf("Precision of reals: %d\n",atoms.getRealPrecision());
+ log.printf("Running over %d %s\n",comm.Get_size(),(comm.Get_size()>1?"nodes":"node"));
+ log.printf("Number of atoms: %d\n",atoms.getNatoms());
+ if(plumedDat.length()>0){
+ readInputFile(plumedDat);
+ plumedDat="";
+ }
+ atoms.updateUnits();
+ log.printf("Timestep: %f\n",atoms.getTimeStep());
+}
+
+void PlumedMain::readInputFile(std::string str){
+ assert(initialized);
+ log.printf("FILE: %s\n",str.c_str());
+ FILE*fp=fopen(str.c_str(),"r");
+ std::vector<std::string> words;
+ while(Tools::getParsedLine(fp,words)){
+ if(words.size()==0)continue;
+ else if(words[0]=="ENDPLUMED") break;
+ else if(words[0]=="LOAD"){
+ std::string s=words[1];
+ assert(words.size()==2);
+ void *p=plumed_dlopen(s.c_str());
+ if(!p){
+// try with different extension
+ size_t n=s.find_last_of(".");
+ if(n==std::string::npos) s+=".";
+ else s=s.substr(0,n+1);
+ s+=soext;
+ p=plumed_dlopen(s.c_str());
+ }
+ if(!p){
+ log<<"ERROR\n";
+ log<<"I cannot load library "<<words[1].c_str()<<"\n";
+ this->exit(1);
+ }
+ log<<"Loading shared library "<<s.c_str()<<"\n";
+ log<<"Here is the new list of available actions\n";
+ actionRegister().log(log);
+ } else if(words[0]=="INCLUDE"){
+ assert(words.size()==2);
+ readInputFile(words[1]);
+ continue;
+ } else {
+ Action* action=actionRegister().create(ActionOptions(*this,words));
+ if(!action){
+ log<<"ERROR\n";
+ log<<"I cannot understand line:";
+ for(unsigned i=0;i<words.size();++i) log<<" "<<words[i];
+ log<<"\n";
+ exit(1);
+ };
+ actionSet.push_back(action);
+ };
+ };
+ fclose(fp);
+ log.printf("END FILE: %s\n",str.c_str());
+
+ pilots=actionSet.select<ActionPilot*>();
+}
+
+
+
+void PlumedMain::calc(){
+ prepareCalc();
+ performCalc();
+}
+
+void PlumedMain::prepareDependencies(){
+
+ active=false;
+
+ atoms.setCollectEnergy(false);
+
+// activate all the actions which are on step
+// activation is recursive and enables also the dependencies
+ for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();p++){
+ (*p)->deactivate();
+ if(Colvar *c=dynamic_cast<Colvar*>(*p)) {
+ if(c->checkIsEnergy()) atoms.setCollectEnergy(true);
+ }
+ }
+
+ for(unsigned i=0;i<pilots.size();++i){
+ if(pilots[i]->onStep()){
+ pilots[i]->activate();
+ active=true;
+ }
+ };
+}
+
+void PlumedMain::shareData(){
+ if(active)atoms.share();
+}
+
+
+void PlumedMain::prepareCalc(){
+ prepareDependencies();
+ shareData();
+}
+
+void PlumedMain::performCalc(){
+
+ if(!active)return;
+ atoms.wait();
+
+// calculate the active actions in order (assuming *backward* dependence)
+ for(ActionSet::iterator p=actionSet.begin();p!=actionSet.end();++p){
+ {
+ ActionWithValue*a=dynamic_cast<ActionWithValue*>(*p);
+ if(a) a->clearInputForces();
+ if(a) a->clearDerivatives();
+ }
+ {
+ ActionAtomistic*a=dynamic_cast<ActionAtomistic*>(*p);
+ if(a) a->clearOutputForces();
+ }
+ if((*p)->isActive()){
+ (*p)->calculate();
+ }
+ }
+
+// Finally apply them in reverse order
+ for(ActionSet::reverse_iterator p=actionSet.rbegin();p!=actionSet.rend();++p){
+ if((*p)->isActive()) (*p)->apply();
+ }
+
+// And update forces:
+ atoms.updateForces();
+
+}
+
+void PlumedMain::exit(int c){
+ comm.Abort(c);
+}
+
+Log& PlumedMain::getLog(){
+ return log;
+}
+
+
+
+
+
diff --git a/src/PlumedMain.h b/src/PlumedMain.h
new file mode 100644
index 000000000..d3fc307e6
--- /dev/null
+++ b/src/PlumedMain.h
@@ -0,0 +1,135 @@
+#ifndef __PLUMED_PlumedMain_h
+#define __PLUMED_PlumedMain_h
+
+#include <string>
+#include <vector>
+#include <set>
+#include "ActionSet.h"
+#include "Atoms.h"
+#include "PlumedCommunicator.h"
+
+
+// !!!!!!!!!!!!!!!!!!!!!! DANGER !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11
+// THE FOLLOWING ARE DEFINITIONS WHICH ARE NECESSARY FOR DYNAMIC LOADING OF THE PLUMED KERNEL:
+// This section should be consistent with the Plumed.h file.
+// Since the Plumed.h file may be included in host MD codes, **NEVER** MODIFY THE CODE DOWN HERE
+
+/* Generic function pointer */
+typedef void (*plumed_function_pointer)(void);
+
+/* Holder for function pointer */
+typedef struct {
+ plumed_function_pointer p;
+} plumed_function_holder;
+
+// END OF DANGER
+////////////////////////////////////////////////////////////
+
+namespace PLMD {
+
+
+
+class ActionAtomistic;
+class ActionPilot;
+class Log;
+
+/// Main plumed object.
+/// In MD engines this object is not manipulated directly but it is wrapped in
+/// plumed or PLMD::Plumed objects. Its main method is cmd(),
+/// which defines completely the external plumed interface.
+/// It does not contain any static data.
+class PlumedMain
+{
+public:
+/// Communicator for plumed.
+/// Includes all the processors used by plumed.
+ PlumedCommunicator comm;
+
+private:
+/// Flag to avoid double initialization
+ bool initialized;
+/// Name of MD engine
+ std::string MDEngine;
+/// Log stream
+ Log log;
+
+
+/// Present step number.
+ int step;
+
+/// Condition for plumed to be active.
+/// At every step, PlumedMain is checking if there are Action's requiring some work.
+/// If at least one Action requires some work, this variable is set to true.
+ bool active;
+
+/// Name of the input file
+ std::string plumedDat;
+
+/// Set of actions found in plumed.dat file
+ ActionSet actionSet;
+
+/// Set of Pilot actions.
+/// These are the action the, if they are Pilot::onStep(), can trigger execution
+ std::vector<ActionPilot*> pilots;
+
+/// Object containing information about atoms (such as positions,...).
+ Atoms atoms; // atomic coordinates
+
+public:
+/// Flag to switch off virial calculation (for debug)
+ bool novirial;
+
+public:
+ PlumedMain();
+/// cmd method, accessible with standard Plumed.h interface.
+/// It is called as plumed_cmd() or as PLMD::Plumed::cmd()
+/// It is the interpreter for plumed commands. It basically contains the definition of the plumed interface.
+/// If you want to add a new functionality to the interface between plumed
+/// and an MD engine, this is the right place
+/// Notice that this interface should always keep retro-compatibility
+ void cmd(const char*key,const void*val=NULL);
+ ~PlumedMain(){};
+/// Read an input file.
+/// \param str name of the file
+ void readInputFile(std::string str);
+/// Initialize the object
+ void init();
+/// Prepare the calculation.
+/// Here it is checked which are the active Actions and communication of the relevant atoms is initiated
+ void prepareCalc();
+ void prepareDependencies();
+ void shareData();
+/// Perform the calculation.
+/// Here atoms coordinates are received and all Action's are applied in order
+ void performCalc();
+/// Shortcut for prepareCalc() + performCalc()
+ void calc();
+/// Reference to atoms object
+ Atoms& getAtoms();
+/// Reference to the list of Action's
+ const ActionSet & getActionSet()const;
+/// Referenge to the log stream
+ Log & getLog();
+/// Return the number of the step
+ const int & getStep()const{return step;};
+/// Stop the run
+ void exit(int c=0);
+};
+
+/////
+// FAST INLINE METHODS:
+
+inline
+const ActionSet & PlumedMain::getActionSet()const{
+ return actionSet;
+}
+
+inline
+Atoms& PlumedMain::getAtoms(){
+ return atoms;
+}
+
+}
+
+#endif
+
diff --git a/src/PlumedStatic.cpp b/src/PlumedStatic.cpp
new file mode 100644
index 000000000..d2aaaa8bd
--- /dev/null
+++ b/src/PlumedStatic.cpp
@@ -0,0 +1,8 @@
+/*
+ We here compile a version of Plumed.c which is statically bound to the plumed library,
+ for which it is not possible to redefine the location of plumed kernel at runtime.
+ Since Plumed.c can be compiled with both C and C++, we opt here for C++
+ so as to further check compatibilities
+*/
+#define __PLUMED_STATIC_KERNEL
+#include "Plumed.c"
diff --git a/src/Print.cpp b/src/Print.cpp
new file mode 100644
index 000000000..ca722789c
--- /dev/null
+++ b/src/Print.cpp
@@ -0,0 +1,109 @@
+#include "ActionPilot.h"
+#include "ActionWithArguments.h"
+#include "ActionRegister.h"
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC GENERIC PRINT
+/**
+Print quantities on file
+
+This action is used to periodically print quantities on a file.
+Similarly to Actions of type \ref Bias, it accepts keywords
+ARG and STRIDE to specify which quantities should be printed and
+how frequently. It also accepts a keyword FMT specifying (in printf() style)
+the format for the written numbers and a keyword FILE specifying the
+name of the output file (if omitted, plumed log will be used).
+This directive can be used multiple times to write multiple files,
+perhaps at different stride.
+
+Example
+\verbatim
+DISTANCE ATOMS=0,10 LABEL=distance
+ENERGY LABEL=energy
+
+# this is writing distance on file COLVAR every 10 steps
+PRINT ARG=distance STRIDE=10 FILE=COLVAR
+# this is writing distance and energy on file COLVAR_ALL every 1000 steps
+PRINT ARG=distance,energy STRIDE=1000 FILE=COLVAR_ALL
+\endverbatim
+
+*/
+//+ENDPLUMEDOC
+
+class Print :
+public ActionPilot,
+public ActionWithArguments
+{
+ string file;
+ FILE* fp;
+ string fmt;
+public:
+ void calculate();
+ Print(const ActionOptions&);
+ void apply(){};
+ void flush();
+ ~Print();
+};
+
+PLUMED_REGISTER_ACTION(Print,"PRINT")
+
+Print::Print(const ActionOptions&ao):
+Action(ao),
+ActionPilot(ao),
+ActionWithArguments(ao),
+fp(NULL),
+fmt("%f")
+{
+ parse("FILE",file);
+ if(file.length()>0){
+ if(comm.Get_rank()==0){
+ fp=fopen(file.c_str(),"wa");
+ log.printf(" on file %s\n",file.c_str());
+ fprintf(fp,"#! FIELDS time");
+ const std::vector<Value*>& arguments(getArguments());
+ for(unsigned i=0;i<arguments.size();i++){
+ fprintf(fp," %s",arguments[i]->getFullName().c_str());
+ };
+ fprintf(fp,"\n");
+ }
+ } else {
+ log.printf(" on plumed log file\n");
+ }
+ parse("FMT",fmt);
+ fmt=" "+fmt;
+ log.printf(" with format %s\n",fmt.c_str());
+ checkRead();
+}
+
+
+void Print::calculate(){
+ if(comm.Get_rank()!=0)return;
+ if(!fp){
+ log.printf("PRINT:");
+ for(unsigned i=0;i<getNumberOfArguments();i++){
+ log.printf(fmt.c_str(),getArgument(i));
+ };
+ log.printf("\n");
+ } else {
+ fprintf(fp," %f",getTime());
+ for(unsigned i=0;i<getNumberOfArguments();i++){
+ fprintf(fp,fmt.c_str(),getArgument(i));
+ };
+ fprintf(fp,"\n");
+ }
+}
+
+Print::~Print(){
+ if(fp) fclose(fp);
+}
+
+void Print::flush(){
+ if(fp) fflush(fp);
+}
+
+}
+
+
diff --git a/src/Tensor.h b/src/Tensor.h
new file mode 100644
index 000000000..ee43aac57
--- /dev/null
+++ b/src/Tensor.h
@@ -0,0 +1,148 @@
+#ifndef __PLUMED_Tensor_h
+#define __PLUMED_Tensor_h
+
+#include "Vector.h"
+
+namespace PLMD{
+
+/// 3x3 matrix of double.
+/// Useful to simplify syntax. All the methods are inlined for better optimization.
+class Tensor{
+ double d[3][3];
+public:
+/// scale the tensor by a factor s
+ friend Tensor operator*(double,const Tensor&);
+/// initialize the tensor to zero
+ Tensor();
+/// initialize a tensor as an external product of two Vector
+ Tensor(const Vector&v1,const Vector&v2);
+/// access element
+ double & operator() (int i,int j);
+/// access element
+ const double & operator() (int i,int j)const;
+/// set it to zero
+ void clear();
+/// returns the determinant
+ double determinant()const;
+/// return an identity tensor
+ static Tensor identity();
+/// return the matrix inverse
+ Tensor inverse()const;
+ Tensor transpose()const;
+};
+
+/// matrix multiplication
+Tensor matmul(const Tensor&,const Tensor&);
+
+Vector matmul(const Tensor&,const Vector&);
+Vector matmul(const Vector&,const Tensor&);
+
+
+inline
+Tensor::Tensor(){
+ for(int i=0;i<3;i++)for(int j=0;j<3;j++)d[i][j]=0.0;
+}
+
+inline
+Tensor::Tensor(const Vector&v1,const Vector&v2){
+ for(int i=0;i<3;i++)for(int j=0;j<3;j++)d[i][j]=v1[i]*v2[j];
+}
+
+inline
+double & Tensor::operator() (int i,int j){
+ return d[i][j];
+}
+
+inline
+const double & Tensor::operator() (int i,int j)const{
+ return d[i][j];
+}
+
+inline
+void Tensor::clear(){
+ d[0][0]=0.0;
+ d[0][1]=0.0;
+ d[0][2]=0.0;
+ d[1][0]=0.0;
+ d[1][1]=0.0;
+ d[1][2]=0.0;
+ d[2][0]=0.0;
+ d[2][1]=0.0;
+ d[2][2]=0.0;
+}
+
+inline
+double Tensor::determinant()const{
+ return
+ d[0][0]*d[1][1]*d[2][2]
+ + d[0][1]*d[1][2]*d[2][0]
+ + d[0][2]*d[1][0]*d[2][1]
+ - d[0][0]*d[1][2]*d[2][1]
+ - d[0][1]*d[1][0]*d[2][2]
+ - d[0][2]*d[1][1]*d[2][0];
+}
+
+inline
+Tensor Tensor::identity(){
+ Tensor t;
+ t(0,0)=1.0;
+ t(1,1)=1.0;
+ t(2,2)=1.0;
+ return t;
+}
+
+inline
+Tensor Tensor::transpose()const{
+ Tensor t;
+ for(int i=0;i<3;i++)for(int j=0;j<3;j++) t(i,j)=d[j][i];
+ return t;
+}
+
+
+inline
+Tensor operator*(double s,const Tensor&v){
+ Tensor t;
+ for(int i=0;i<3;i++)for(int j=0;j<3;j++) t(i,j)=s*v(i,j);
+ return t;
+}
+
+inline
+Tensor Tensor::inverse()const{
+ Tensor t;
+ double invdet=1.0/determinant();
+ for(int i=0;i<3;i++) for(int j=0;j<3;j++)
+ t(j,i)=invdet*( d[(i+1)%3][(j+1)%3]*d[(i+2)%3][(j+2)%3]
+ -d[(i+1)%3][(j+2)%3]*d[(i+2)%3][(j+1)%3]);
+ return t;
+}
+
+inline
+Tensor matmul(const Tensor&a,const Tensor&b){
+ Tensor t;
+ for(int i=0;i<3;i++) for(int j=0;j<3;j++) for(int k=0;k<3;k++) {
+ t(i,j)+=a(i,k)*b(k,j);
+ }
+ return t;
+}
+
+inline
+Vector matmul(const Tensor&a,const Vector&b){
+ Vector t;
+ for(int i=0;i<3;i++) for(int j=0;j<3;j++) t(i)+=a(i,j)*b(j);
+ return t;
+}
+
+inline
+Vector matmul(const Vector&a,const Tensor&b){
+ Vector t;
+ for(int i=0;i<3;i++) for(int j=0;j<3;j++) t(i)+=a(i)*b(i,j);
+ return t;
+}
+
+
+
+
+}
+
+#endif
+
diff --git a/src/Tools.cpp b/src/Tools.cpp
new file mode 100644
index 000000000..361488fb6
--- /dev/null
+++ b/src/Tools.cpp
@@ -0,0 +1,117 @@
+#include "Tools.h"
+#include <cstring>
+#include <assert.h>
+#include <sstream>
+
+using namespace PLMD;
+using namespace std;
+
+#define IMPLEMENT(T) \
+bool Tools::convert(const string & str,T & t){ \
+ istringstream istr(str.c_str()); \
+ bool ok=istr>>t; \
+ if(!ok) return false; \
+ string remaining; \
+ istr>>remaining; \
+ return remaining.length()==0; \
+}
+
+IMPLEMENT(double)
+IMPLEMENT(int)
+
+bool Tools::convert(const string & str,string & t){
+ t=str;
+ return true;
+}
+
+vector<string> Tools::getWords(const string & line,const char* separators){
+ char* ww;
+ char* s3;
+ char* copy;
+ copy= new char[strlen(line.c_str())+1];
+ strcpy(copy,line.c_str());
+ vector<string> words;
+ ww=strtok_r(copy,separators,&s3);
+ if(ww){
+ words.push_back(string(ww));
+ while((ww=strtok_r(NULL,separators,&s3))) words.push_back(string(ww));
+ }
+ delete [] copy;
+ return words;
+}
+
+bool Tools::getParsedLine(FILE* fp,vector<string> & words){
+ string line("");
+ words.clear();
+ bool stat;
+ bool inside=false;
+ while(stat=getline(fp,line)){
+ trimComments(line);
+ trim(line);
+ if(line.length()==0) continue;
+ vector<string> w=getWords(line);
+ if(w.size()==0) continue;
+ if(inside && *(w.begin())=="..."){
+ inside=false;
+ if(w.size()==2) assert(w[1]==words[0]);
+ assert(w.size()<=2);
+ w.clear();
+ }else if(*(w.end()-1)=="..."){
+ inside=true;
+ w.erase(w.end()-1);
+ };
+ for(unsigned i=0;i<w.size();++i) words.push_back(w[i]);
+ if(!inside)break;
+ }
+ if(words.size()>0) return true;
+ return stat;
+}
+
+
+bool Tools::getline(FILE* fp,string & line){
+ line="";
+ const int bufferlength=5;
+ char buffer[bufferlength];
+ bool ret;
+ while(ret=fgets(buffer,bufferlength,fp)){
+ line.append(buffer);
+ if(buffer[strlen(buffer)-1]=='\n') break;
+ };
+ if(*(line.end()-1)=='\n') line.erase(line.end()-1);
+ return ret;
+}
+
+void Tools::trim(string & s){
+ size_t n=s.find_last_not_of(" \t");
+ s=s.substr(0,n+1);
+}
+
+void Tools::trimComments(string & s){
+ size_t n=s.find_first_of("#");
+ s=s.substr(0,n);
+}
+
+bool Tools::getKey(vector<string>& line,const string & key,string & s){
+ s.clear();
+ for(vector<string>::iterator p=line.begin();p!=line.end();++p){
+ if((*p).length()==0) continue;
+ string x=(*p).substr(0,key.length());
+ if(x==key){
+ if((*p).length()==key.length())return false;
+ string tmp=(*p).substr(key.length(),(*p).length());
+ line.erase(p);
+ s=tmp;
+ return true;
+ }
+ };
+ return true;
+}
+
+void Tools::convert(int i,std::string & str){
+ std::ostringstream ostr;
+ ostr<<i;
+ str=ostr.str();
+}
+
+
+
diff --git a/src/Tools.h b/src/Tools.h
new file mode 100644
index 000000000..20a18d9ce
--- /dev/null
+++ b/src/Tools.h
@@ -0,0 +1,103 @@
+#ifndef __PLUMED_Tools_h
+#define __PLUMED_Tools_h
+
+#include <vector>
+#include <string>
+#include <cstdio>
+#include <cmath>
+#include <limits>
+
+namespace PLMD{
+
+const double epsilon(std::numeric_limits<double>::epsilon());
+
+/// Empty class which just contains several (static) tools
+class Tools{
+public:
+ static std::vector<std::string> getWords(const std::string & line,const char* sep=" \t\n");
+ static std::vector<std::string> getWords(const std::string & line,const char* sep,const char* quote);
+ static bool getline(std::FILE* fp,std::string & line);
+ static bool getParsedLine(std::FILE* fp,std::vector<std::string> & line);
+ static bool convert(const std::string & str,double & t);
+ static bool convert(const std::string & str,int & t);
+ static bool convert(const std::string & str,std::string & t);
+ static void convert(int i,std::string & str);
+ static void trim(std::string & s);
+ static void trimComments(std::string & s);
+
+
+ static double pbc(double);
+
+ static bool getKey(std::vector<std::string>& line,const std::string & key,std::string & s);
+
+ template <class T>
+ static bool parse(std::vector<std::string>&line,const std::string&key,T&val);
+ template <class T>
+ static bool parseVector(std::vector<std::string>&line,const std::string&key,std::vector<T>&val);
+ static bool parseFlag(std::vector<std::string>&line,const std::string&key,bool&val);
+
+ template <class T>
+ static double getArray(void*,int,int,double);
+ template <class T>
+ static double getArray(void*,void*,void*,int,int,double);
+};
+
+template <class T>
+bool Tools::parse(std::vector<std::string>&line,const std::string&key,T&val){
+ std::string s;
+ if(!getKey(line,key+"=",s)) return false;
+ if(s.length()>0 && !convert(s,val))return false;
+ return true;
+}
+
+template <class T>
+bool Tools::parseVector(std::vector<std::string>&line,const std::string&key,std::vector<T>&val){
+ std::string s;
+ if(!getKey(line,key+"=",s)) return false;
+ if(s.length()==0) return true;
+ val.clear();
+ std::vector<std::string> words=getWords(s,",");
+ for(unsigned i=0;i<words.size();++i){
+ T v;
+ if(!convert(words[i],v))return false;
+ val.push_back(v);
+ }
+ return true;
+}
+
+inline
+bool Tools::parseFlag(std::vector<std::string>&line,const std::string&key,bool&val){
+ std::string s;
+ for(std::vector<std::string>::iterator p=line.begin();p!=line.end();++p){
+ if(key==*p){
+ val=true;
+ line.erase(p);
+ return true;
+ }
+ }
+ return true;
+}
+
+template <class T>
+double Tools::getArray(void*p,int iat,int idim,double scale){
+ return (static_cast<T*>(p))[3*iat+idim]*scale;
+}
+
+template <class T>
+double Tools::getArray(void*px,void*py,void*pz,int iat,int idim,double scale){
+ if(idim==0) return (static_cast<T*>(px))[iat]*scale;
+ if(idim==1) return (static_cast<T*>(py))[iat]*scale;
+ return (static_cast<T*>(pz))[iat]*scale;
+}
+
+inline
+double Tools::pbc(double x){
+ return x-floor(x+0.5);
+}
+
+
+
+}
+
+#endif
+
diff --git a/src/Units.cpp b/src/Units.cpp
new file mode 100644
index 000000000..229dcb133
--- /dev/null
+++ b/src/Units.cpp
@@ -0,0 +1,133 @@
+#include "ActionSetup.h"
+#include "ActionRegister.h"
+#include "PlumedMain.h"
+
+using namespace std;
+
+namespace PLMD{
+
+//+PLUMEDOC GENERIC UNITS
+/**
+Sets internal units.
+
+This Action is used to set internal units for PLUMED. It accepts
+the keywords LENGTH, TIME and ENERGY, fixing the units of
+the corresponding quantity. All the other quantities are derived,
+e.g. forces are measured in ENERGY/LENGTH. The following
+values are accepted:
+- LENGTH
+ - nm (default)
+ - A
+ - um
+- ENERGY
+ - kj/mol (default)
+ - j/mol
+ - kcal/mol
+- TIME
+ - ps (default)
+ - ns
+ - fs
+
+This directive needs to be used at the beginning of the plumed.dat file,
+before any other directive which may take as input a quantity measured
+in the aforementioned units.
+
+\verbatim
+# this is using nm - kj/mol - fs
+UNITS LENGTH=nm TIME=fs
+\endverbatim
+
+If a number is found, it is interpreted as a multiplication
+with respect to the default
+\verbatim
+# this is using nm - kj/mol - fs
+UNITS LENGTH=nm TIME=0.001
+\endverbatim
+
+
+*/
+//+ENDPLUMEDOC
+
+class Units :
+ public ActionSetup
+{
+public:
+ Units(const ActionOptions&ao);
+};
+
+PLUMED_REGISTER_ACTION(Units,"UNITS")
+
+Units::Units(const ActionOptions&ao):
+Action(ao),
+ActionSetup(ao)
+{
+ double length=1.0;
+ double energy=1.0;
+ double time=1.0;
+
+ std::string s;
+ bool numeric;
+
+ s="nm";
+ numeric=false;
+ parse("LENGTH",s);
+ if(s=="nm"){
+ length=1.0;
+ } else if(s=="A"){
+ length=0.1;
+ } else if(s=="um"){
+ length=1000.0;
+ } else {
+ length=-1.0;
+ Tools::convert(s,length);
+ numeric=true;
+ assert(length>0.0);
+ }
+ if(!numeric) log.printf(" length: %s\n",s.c_str());
+ else log.printf(" length: %f nm\n",length);
+
+ s="kj/mol";
+ numeric=false;
+ parse("ENERGY",s);
+ if(s=="kj/mol"){
+ energy=1.0;
+ } else if(s=="kcal/mol"){
+ energy=4.184;
+ } else if(s=="j/mol"){
+ energy=0.001;
+ } else {
+ energy=-1.0;
+ Tools::convert(s,energy);
+ numeric=true;
+ assert(energy>0.0);
+ }
+ if(!numeric) log.printf(" energy: %s\n",s.c_str());
+ else log.printf(" energy: %f kj/mol\n",energy);
+
+ s="ps";
+ numeric=false;
+ parse("TIME",s);
+ if(s=="ps"){
+ time=1.0;
+ } else if(s=="ns"){
+ time=1000.0;
+ } else if(s=="fs"){
+ time=0.001;
+ } else {
+ time=-1.0;
+ Tools::convert(s,time);
+ numeric=true;
+ assert(time>0.0);
+ }
+ if(!numeric) log.printf(" time: %s\n",s.c_str());
+ else log.printf(" energy: %f ns\n",time);
+
+ checkRead();
+
+ plumed.getAtoms().setInternalLengthUnits(length);
+ plumed.getAtoms().setInternalEnergyUnits(energy);
+ plumed.getAtoms().setInternalTimeUnits(time);
+}
+
+}
+
diff --git a/src/Value.cpp b/src/Value.cpp
new file mode 100644
index 000000000..f95b594e0
--- /dev/null
+++ b/src/Value.cpp
@@ -0,0 +1,15 @@
+#include "Value.h"
+#include "ActionWithValue.h"
+
+using namespace PLMD;
+
+const std::string Value::getFullName()const{
+ return action.getLabel()+"."+name;
+}
+
+void Value::enableDerivatives()
+{
+ deriv=true;derivatives.resize(action.getNumberOfParameters());
+}
+
+
diff --git a/src/Value.h b/src/Value.h
new file mode 100644
index 000000000..b8b853a92
--- /dev/null
+++ b/src/Value.h
@@ -0,0 +1,47 @@
+#ifndef __PLUMED_Value_h
+#define __PLUMED_Value_h
+
+#include <vector>
+#include <string>
+#include <cassert>
+
+
+namespace PLMD{
+
+class ActionWithValue;
+
+/// Class containing a value which can be addressed by PLMD::ActionWithArguments.
+/// It also contains the derivative of this value with respect to
+/// an arbitrary number of parameters.
+/// Typically, an object of type PLMD::ActionWithValue will contain one or
+/// more objects of type PLUMD::Value, one per component.
+class Value{
+ ActionWithValue&action;
+ double value;
+ double inputForce;
+ std::vector<double> derivatives;
+ std::string name;
+ bool deriv;
+public:
+ void set(double v){value=v;}
+ void setValue(double v){value=v;}
+ double getValue()const{return value;}
+ const std::string& getName()const{return name;}
+ const std::string getFullName()const;
+ Value(ActionWithValue&action,const std::string& name):action(action),value(0.0),name(name),deriv(false){};
+ void enableDerivatives();
+ bool hasDerivatives(){return deriv;};
+ void setNumberOfParameters(int n){if(deriv)derivatives.resize(n);}
+ void setDerivatives(int i,double d){derivatives[i]=d;}
+ void clearInputForce(){inputForce=0.0;}
+ void clearDerivatives(){derivatives.assign(derivatives.size(),0.0);}
+ double getForce()const{return inputForce;}
+ void addForce(double f){assert(hasDerivatives());inputForce+=f;}
+ const std::vector<double> & getDerivatives()const{return derivatives;}
+ ActionWithValue& getAction(){return action;};
+};
+
+}
+
+#endif
+
diff --git a/src/Vector.cpp b/src/Vector.cpp
new file mode 100644
index 000000000..c8ab2b141
--- /dev/null
+++ b/src/Vector.cpp
@@ -0,0 +1,9 @@
+#include "Vector.h"
+#include <cmath>
+
+using namespace PLMD;
+
+double Vector::modulo()const{
+ return sqrt(modulo2());
+}
+
diff --git a/src/Vector.h b/src/Vector.h
new file mode 100644
index 000000000..df89bd89a
--- /dev/null
+++ b/src/Vector.h
@@ -0,0 +1,110 @@
+#ifndef __PLUMED_Vector_h
+#define __PLUMED_Vector_h
+
+namespace PLMD{
+
+/// 3d vector of double.
+/// Useful to simplify syntax. All the methods are inlined for better optimization.
+/// Accepts both [] and () syntax for access.
+class Vector{
+ double d[3];
+public:
+/// return v2-v1
+ friend Vector delta(const Vector&v1,const Vector&v2);
+/// return s*v
+ friend Vector operator*(double,const Vector&);
+/// return v1+v2
+ friend Vector operator+(const Vector&,const Vector&);
+/// array-like access [i]
+ double & operator[](int i);
+/// array-like access [i]
+ const double & operator[](int i)const;
+/// parenthesis access (i)
+ double & operator()(int i);
+/// parenthesis access (i)
+ const double & operator()(int i)const;
+/// set it to zero
+ void clear();
+/// create it with components x0, x1 and x2
+ Vector(double x0,double x1,double x2);
+/// create it null
+ Vector();
+/// compute the squared modulo
+ double modulo2()const;
+/// compute the modulo
+ double modulo()const;
+/// scale the vector by a factor s
+ void scale(double s);
+};
+
+inline
+double & Vector::operator[](int i){
+return d[i];
+}
+
+inline
+const double & Vector::operator[](int i)const{
+ return d[i];
+}
+
+inline
+double & Vector::operator()(int i){
+ return d[i];
+}
+
+inline
+const double & Vector::operator()(int i)const{
+ return d[i];
+}
+
+inline
+Vector delta(const Vector&v1,const Vector&v2){
+ return Vector(v2[0]-v1[0],v2[1]-v1[1],v2[2]-v1[2]);
+}
+
+inline
+Vector operator*(double s,const Vector&v){
+ return Vector(s*v[0],s*v[1],s*v[2]);
+}
+
+inline
+void Vector::clear(){
+ d[0]=0.0;
+ d[1]=0.0;
+ d[2]=0.0;
+}
+
+inline
+Vector::Vector(double x0,double x1,double x2){
+ d[0]=x0;
+ d[1]=x1;
+ d[2]=x2;
+}
+
+inline
+Vector::Vector(){
+ d[0]=0.0;
+ d[1]=0.0;
+ d[2]=0.0;
+}
+
+inline
+double Vector::modulo2()const{
+ return d[0]*d[0]+d[1]*d[1]+d[2]*d[2];
+}
+
+inline
+void Vector::scale(double s){
+ d[0]*=s;d[1]*=s;d[2]*=s;
+}
+
+inline
+Vector operator+(const Vector&v1,const Vector&v2){
+ return Vector(v1[0]+v2[0],v1[1]+v2[1],v1[2]+v2[2]);
+}
+
+}
+
+
+#endif
+
diff --git a/test/Makefile b/test/Makefile
new file mode 100644
index 000000000..a8e3b3fed
--- /dev/null
+++ b/test/Makefile
@@ -0,0 +1,15 @@
+-include ../Makefile.conf
+
+SUBDIRS = link simplemd
+
+.PHONY: all clean $(SUBDIRS)
+
+all: $(SUBDIRS)
+
+$(SUBDIRS):
+ $(MAKE) -C $@
+
+clean:
+ cd link && make clean
+ cd simplemd && make clean
+
diff --git a/test/amber/.gitignore b/test/amber/.gitignore
new file mode 100644
index 000000000..e12bdc2ee
--- /dev/null
+++ b/test/amber/.gitignore
@@ -0,0 +1,6 @@
+*
+!amber_input
+!system.inpcrd
+!system.prmtop
+!plumed.dat
+!.gitignore
diff --git a/test/amber/amber_input b/test/amber/amber_input
new file mode 100644
index 000000000..fe7da236d
--- /dev/null
+++ b/test/amber/amber_input
@@ -0,0 +1,11 @@
+METADYNAMICS TEST
+&cntrl
+ imin=0, irest=0, ntx=1, ig=71278 ,
+ nstlim=1001, dt=0.0002,
+ ntc=1, ntf=1,
+ ntt=3, gamma_ln=5 ,
+ tempi=300.0, temp0=300.0,
+ ntpr=200, ntwx=0,
+ ntb=0, igb=0,
+ cut=999., plumed=1 , plumedfile='plumed.dat'
+/
diff --git a/test/amber/plumed.dat b/test/amber/plumed.dat
new file mode 100644
index 000000000..c0be88445
--- /dev/null
+++ b/test/amber/plumed.dat
@@ -0,0 +1,4 @@
+DISTANCE ATOMS=0,10 LABEL=dist
+ENERGY
+RESTRAINT ARG=dist KAPPA=10000 AT=0.3
+PRINT ARG=* FILE=COLVAR
diff --git a/test/amber/system.inpcrd b/test/amber/system.inpcrd
new file mode 100644
index 000000000..b732823e3
--- /dev/null
+++ b/test/amber/system.inpcrd
@@ -0,0 +1,13 @@
+ACE
+ 22
+ 2.0177833 1.0353295 0.0542168 1.9998067 2.1250666 0.0538082
+ 1.4254166 2.4843904 0.9072400 1.5326313 2.4823206 -0.8638698
+ 3.4222907 2.6597886 0.1389017 4.3607216 1.8984493 0.3631598
+ 3.5879191 3.9603571 -0.1138393 2.7859198 4.5436605 -0.3046603
+ 4.8919526 4.5905945 -0.0675145 5.4432975 4.2337999 0.8026422
+ 5.6616692 4.2349396 -1.3354247 5.1089564 4.5854833 -2.2068147
+ 6.6419078 4.7111339 -1.3103306 5.7851258 3.1535202 -1.3931851
+ 4.7222411 6.1004128 0.0215211 3.6035082 6.6057631 -0.0398724
+ 5.8431179 6.8242650 0.0735169 6.7415384 6.3635968 0.0875836
+ 5.8209701 8.2733497 0.0569928 4.7879086 8.6215931 0.0518138
+ 6.3303031 8.6556759 0.9417330 6.3290771 8.6329497 -0.8383083
diff --git a/test/amber/system.prmtop b/test/amber/system.prmtop
new file mode 100644
index 000000000..702853ce1
--- /dev/null
+++ b/test/amber/system.prmtop
@@ -0,0 +1,232 @@
+%VERSION VERSION_STAMP = V0001.000 DATE = 05/31/08 11:43:33
+%FLAG TITLE
+%FORMAT(20a4)
+ACE
+%FLAG POINTERS
+%FORMAT(10I8)
+ 22 7 12 9 25 11 42 24 0 0
+ 99 3 9 11 24 8 16 19 7 0
+ 0 0 0 0 0 0 0 0 10 0
+ 0
+%FLAG ATOM_NAME
+%FORMAT(20a4)
+HH31CH3 HH32HH33C O N H CA HA CB HB1 HB2 HB3 C O N H CH3 HH31
+HH32HH33
+%FLAG CHARGE
+%FORMAT(5E16.8)
+ 2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00 1.08823576E+01
+ -1.03484442E+01 -7.57501011E+00 4.95464337E+00 6.14091510E-01 1.49969529E+00
+ -3.32556975E+00 1.09880469E+00 1.09880469E+00 1.09880469E+00 1.08841798E+01
+ -1.03484442E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00 1.77849648E+00
+ 1.77849648E+00 1.77849648E+00
+%FLAG MASS
+%FORMAT(5E16.8)
+ 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01
+ 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
+ 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01
+ 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00
+ 1.00800000E+00 1.00800000E+00
+%FLAG ATOM_TYPE_INDEX
+%FORMAT(10I8)
+ 1 2 1 1 3 4 5 6 2 7
+ 2 1 1 1 3 4 5 6 2 7
+ 7 7
+%FLAG NUMBER_EXCLUDED_ATOMS
+%FORMAT(10I8)
+ 6 7 4 3 7 3 10 4 10 7
+ 6 3 2 1 7 3 5 4 3 2
+ 1 1
+%FLAG NONBONDED_PARM_INDEX
+%FORMAT(10I8)
+ 1 2 4 7 11 16 22 2 3 5
+ 8 12 17 23 4 5 6 9 13 18
+ 24 7 8 9 10 14 19 25 11 12
+ 13 14 15 20 26 16 17 18 19 20
+ 21 27 22 23 24 25 26 27 28
+%FLAG RESIDUE_LABEL
+%FORMAT(20a4)
+ACE ALA NME
+%FLAG RESIDUE_POINTER
+%FORMAT(10I8)
+ 1 7 17
+%FLAG BOND_FORCE_CONSTANT
+%FORMAT(5E16.8)
+ 5.70000000E+02 4.90000000E+02 3.40000000E+02 3.17000000E+02 3.40000000E+02
+ 3.10000000E+02 4.34000000E+02 3.37000000E+02
+%FLAG BOND_EQUIL_VALUE
+%FORMAT(5E16.8)
+ 1.22900000E+00 1.33500000E+00 1.09000000E+00 1.52200000E+00 1.09000000E+00
+ 1.52600000E+00 1.01000000E+00 1.44900000E+00
+%FLAG ANGLE_FORCE_CONSTANT
+%FORMAT(5E16.8)
+ 8.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01
+ 8.00000000E+01 7.00000000E+01 6.30000000E+01 5.00000000E+01 5.00000000E+01
+ 5.00000000E+01 5.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01
+ 3.50000000E+01
+%FLAG ANGLE_EQUIL_VALUE
+%FORMAT(5E16.8)
+ 2.14501057E+00 2.09439600E+00 2.12755727E+00 1.91113635E+00 1.91113635E+00
+ 2.10137732E+00 2.03505478E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00
+ 1.91113635E+00 2.06018753E+00 1.91113635E+00 1.91462701E+00 1.92160833E+00
+ 1.91113635E+00
+%FLAG DIHEDRAL_FORCE_CONSTANT
+%FORMAT(5E16.8)
+ 2.00000000E+00 2.50000000E+00 0.00000000E+00 2.00000000E+00 4.00000000E-01
+ 0.00000000E+00 0.00000000E+00 2.70000000E-01 4.20000000E-01 8.00000000E-01
+ 8.00000000E-02 1.55555556E-01 2.00000000E-01 2.00000000E-01 4.50000000E-01
+ 1.58000000E+00 5.50000000E-01 1.05000000E+01 1.10000000E+00
+%FLAG DIHEDRAL_PERIODICITY
+%FORMAT(5E16.8)
+ 1.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 3.00000000E+00
+ 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00
+ 3.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00 1.00000000E+00
+ 2.00000000E+00 3.00000000E+00 2.00000000E+00 2.00000000E+00
+%FLAG DIHEDRAL_PHASE
+%FORMAT(5E16.8)
+ 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00
+ 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00
+%FLAG SOLTY
+%FORMAT(5E16.8)
+ 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00
+ 0.00000000E+00 0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF
+%FORMAT(5E16.8)
+ 7.51607703E+03 9.71708117E+04 1.04308023E+06 8.61541883E+04 9.24822270E+05
+ 8.19971662E+05 5.44261042E+04 6.47841731E+05 5.74393458E+05 3.79876399E+05
+ 8.96776989E+04 9.95480466E+05 8.82619071E+05 6.06829342E+05 9.44293233E+05
+ 1.07193646E+02 2.56678134E+03 2.27577561E+03 1.02595236E+03 2.12601181E+03
+ 1.39982777E-01 4.98586848E+03 6.78771368E+04 6.01816484E+04 3.69471530E+04
+ 6.20665997E+04 5.94667300E+01 3.25969625E+03
+%FLAG LENNARD_JONES_BCOEF
+%FORMAT(5E16.8)
+ 2.17257828E+01 1.26919150E+02 6.75612247E+02 1.12529845E+02 5.99015525E+02
+ 5.31102864E+02 1.11805549E+02 6.26720080E+02 5.55666448E+02 5.64885984E+02
+ 1.36131731E+02 7.36907417E+02 6.53361429E+02 6.77220874E+02 8.01323529E+02
+ 2.59456373E+00 2.06278363E+01 1.82891803E+01 1.53505284E+01 2.09604198E+01
+ 9.37598976E-02 1.76949863E+01 1.06076943E+02 9.40505980E+01 9.21192136E+01
+ 1.13252061E+02 1.93248820E+00 1.43076527E+01
+%FLAG BONDS_INC_HYDROGEN
+%FORMAT(10I8)
+ 3 6 3 3 9 3 0 3 3 30
+ 33 3 30 36 3 30 39 3 24 27
+ 5 18 21 7 54 57 5 54 60 5
+ 54 63 5 48 51 7
+%FLAG BONDS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+ 12 15 1 12 18 2 3 12 4 42
+ 45 1 42 48 2 24 30 6 24 42
+ 4 18 24 8 48 54 8
+%FLAG ANGLES_INC_HYDROGEN
+%FORMAT(10I8)
+ 12 18 21 2 9 3 12 4 6 3
+ 9 5 6 3 12 4 0 3 6 5
+ 0 3 9 5 0 3 12 4 42 48
+ 51 2 36 30 39 5 33 30 36 5
+ 33 30 39 5 27 24 30 9 27 24
+ 42 10 24 30 33 11 24 30 36 11
+ 24 30 39 11 21 18 24 12 18 24
+ 27 13 60 54 63 16 57 54 60 16
+ 57 54 63 16 51 48 54 12 48 54
+ 57 13 48 54 60 13 48 54 63 13
+%FLAG ANGLES_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+ 15 12 18 1 12 18 24 3 3 12
+ 15 6 3 12 18 7 45 42 48 1
+ 42 48 54 3 30 24 42 8 24 42
+ 45 6 24 42 48 7 18 24 30 14
+ 18 24 42 15
+%FLAG DIHEDRALS_INC_HYDROGEN
+%FORMAT(10I8)
+ 15 12 18 21 1 15 12 -18 21 2
+ 12 18 24 27 3 9 3 12 15 10
+ 9 3 -12 15 3 9 3 -12 15 11
+ 9 3 12 18 3 6 3 12 15 10
+ 6 3 -12 15 3 6 3 -12 15 11
+ 6 3 12 18 3 3 12 18 21 2
+ 0 3 12 15 10 0 3 -12 15 3
+ 0 3 -12 15 11 0 3 12 18 3
+ 45 42 48 51 1 45 42 -48 51 2
+ 42 48 54 57 3 42 48 54 60 3
+ 42 48 54 63 3 39 30 24 42 12
+ 36 30 24 42 12 33 30 24 42 12
+ 27 24 30 33 12 27 24 30 36 12
+ 27 24 30 39 12 27 24 42 45 10
+ 27 24 -42 45 11 27 24 42 48 3
+ 24 42 48 51 2 21 18 24 27 3
+ 21 18 24 30 3 21 18 24 42 3
+ 18 24 30 33 12 18 24 30 36 12
+ 18 24 30 39 12 51 48 54 57 3
+ 51 48 54 60 3 51 48 54 63 3
+ 12 24 -18 -21 19 42 54 -48 -51 19
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN
+%FORMAT(10I8)
+ 15 12 18 24 2 12 18 24 30 1
+ 12 18 -24 30 4 12 18 -24 30 5
+ 12 18 -24 30 6 12 18 24 42 7
+ 12 18 -24 42 8 12 18 -24 42 9
+ 12 18 -24 42 6 3 12 18 24 2
+ 45 42 48 54 2 30 24 42 45 3
+ 30 24 42 48 13 30 24 -42 48 14
+ 30 24 -42 48 5 30 24 -42 48 6
+ 24 42 48 54 2 18 24 42 45 3
+ 18 24 42 48 15 18 24 -42 48 16
+ 18 24 -42 48 17 18 24 -42 48 6
+ 3 18 -12 -15 18 24 48 -42 -45 18
+%FLAG EXCLUDED_ATOMS_LIST
+%FORMAT(10I8)
+ 2 3 4 5 6 7 3 4 5 6
+ 7 8 9 4 5 6 7 5 6 7
+ 6 7 8 9 10 11 15 7 8 9
+ 8 9 10 11 12 13 14 15 16 17
+ 9 10 11 15 10 11 12 13 14 15
+ 16 17 18 19 11 12 13 14 15 16
+ 17 12 13 14 15 16 17 13 14 15
+ 14 15 15 16 17 18 19 20 21 22
+ 17 18 19 18 19 20 21 22 19 20
+ 21 22 20 21 22 21 22 22 0
+%FLAG HBOND_ACOEF
+%FORMAT(5E16.8)
+
+%FLAG HBOND_BCOEF
+%FORMAT(5E16.8)
+
+%FLAG HBCUT
+%FORMAT(5E16.8)
+
+%FLAG AMBER_ATOM_TYPE
+%FORMAT(20a4)
+HC CT HC HC C O N H CT H1 CT HC HC HC C O N H CT H1
+H1 H1
+%FLAG TREE_CHAIN_CLASSIFICATION
+%FORMAT(20a4)
+M M E E M E M E M E 3 E E E M E M E M E
+E E
+%FLAG JOIN_ARRAY
+%FORMAT(10I8)
+ 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0
+ 0 0
+%FLAG IROTAT
+%FORMAT(10I8)
+ 0 0 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0 0 0
+ 0 0
+%FLAG RADIUS_SET
+%FORMAT(1a80)
+modified Bondi radii (mbondi)
+%FLAG RADII
+%FORMAT(5E16.8)
+ 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
+ 1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
+ 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00
+ 1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00
+ 1.30000000E+00 1.30000000E+00
+%FLAG SCREEN
+%FORMAT(5E16.8)
+ 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
+ 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
+ 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01
+ 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01
+ 8.50000000E-01 8.50000000E-01
diff --git a/test/gromacs/.gitignore b/test/gromacs/.gitignore
new file mode 100644
index 000000000..ed46248f4
--- /dev/null
+++ b/test/gromacs/.gitignore
@@ -0,0 +1,6 @@
+*
+!grompp.mdp
+!conf.gro
+!topol.top
+!plumed.dat
+!.gitignore
diff --git a/test/gromacs/conf.gro b/test/gromacs/conf.gro
new file mode 100644
index 000000000..b50d3e2c5
--- /dev/null
+++ b/test/gromacs/conf.gro
@@ -0,0 +1,652 @@
+Protein in water
+ 649
+ 1ACE CH3 1 1.395 0.076 0.303 -0.5810 -0.4924 0.0391
+ 1ACE HH31 2 1.313 0.018 0.262 0.2172 -2.6470 1.3107
+ 1ACE HH32 3 1.453 0.126 0.226 -2.6835 0.3294 -1.0497
+ 1ACE HH33 4 1.458 0.004 0.356 1.8282 1.1665 -0.4057
+ 1ACE C 5 1.357 0.171 0.416 0.0337 -0.5699 0.3099
+ 1ACE O 6 1.244 0.184 0.460 -0.1333 -0.2640 -0.2087
+ 2ALA N 7 1.456 0.250 0.459 -0.4673 0.3285 -0.1890
+ 2ALA H 8 1.549 0.244 0.420 -0.4960 -1.3002 -0.0375
+ 2ALA CA 9 1.439 0.352 0.561 -0.5349 -0.1719 0.2994
+ 2ALA HA 10 1.385 0.316 0.648 -0.0171 -0.7928 0.3660
+ 2ALA CB 11 1.576 0.397 0.613 -0.5920 0.2975 0.0363
+ 2ALA HB1 12 1.636 0.314 0.649 1.5040 1.7138 -0.0305
+ 2ALA HB2 13 1.636 0.434 0.530 0.3715 -0.6825 0.2893
+ 2ALA HB3 14 1.574 0.461 0.701 -0.4708 -1.3463 1.2681
+ 2ALA C 15 1.375 0.479 0.507 0.2320 0.0944 0.0067
+ 2ALA O 16 1.328 0.573 0.570 0.2877 0.1064 0.0239
+ 3NAC N 17 1.361 0.489 0.374 -0.0686 0.1189 0.0416
+ 3NAC H 18 1.422 0.419 0.332 -0.2524 0.0522 -0.1064
+ 3NAC CH3 19 1.284 0.582 0.295 -0.4648 -0.3751 -0.1488
+ 3NAC HH31 20 1.259 0.675 0.346 0.8612 -0.5690 0.9097
+ 3NAC HH32 21 1.352 0.610 0.214 -1.0347 2.4348 0.2432
+ 3NAC HH33 22 1.193 0.542 0.250 -0.2661 0.4329 -1.3265
+ 4SOL OW 23 0.601 0.389 0.219 0.4328 -0.0094 -0.2171
+ 4SOL HW1 24 0.648 0.462 0.178 1.0458 -0.2789 -0.0095
+ 4SOL HW2 25 0.563 0.341 0.145 2.7889 -1.3555 -0.6932
+ 5SOL OW 26 1.624 1.747 1.860 0.3011 -0.0959 -0.9133
+ 5SOL HW1 27 1.697 1.783 1.912 0.0600 -0.3559 -0.4003
+ 5SOL HW2 28 1.666 1.714 1.781 0.5887 0.8936 -1.1902
+ 6SOL OW 29 0.506 0.057 0.281 -0.5106 -0.6150 -0.0615
+ 6SOL HW1 30 0.518 -0.014 0.344 1.5419 0.2809 0.6323
+ 6SOL HW2 31 0.594 0.075 0.248 -1.0909 1.1100 -0.7698
+ 7SOL OW 32 0.756 0.086 0.134 0.9247 -0.2288 -0.5202
+ 7SOL HW1 33 0.780 -0.007 0.141 -0.7854 -0.6032 1.0074
+ 7SOL HW2 34 0.839 0.132 0.140 1.9256 -1.6657 -2.3114
+ 8SOL OW 35 0.793 0.668 0.345 -0.3163 -0.4667 -0.7345
+ 8SOL HW1 36 0.829 0.604 0.407 -0.7251 -0.1866 -0.2022
+ 8SOL HW2 37 0.799 0.624 0.260 1.3029 -0.4247 -0.6803
+ 9SOL OW 38 0.448 1.243 1.246 0.1594 -0.1188 -0.0978
+ 9SOL HW1 39 0.453 1.301 1.322 0.2338 0.0416 -0.2300
+ 9SOL HW2 40 0.529 1.191 1.250 -0.3010 -0.8077 0.5020
+ 10SOL OW 41 1.477 1.311 0.950 -0.0745 0.0419 0.4465
+ 10SOL HW1 42 1.402 1.366 0.925 0.2388 0.1665 -0.2275
+ 10SOL HW2 43 1.552 1.371 0.946 -0.0635 0.1704 2.1023
+ 11SOL OW 44 1.173 0.766 0.978 0.1154 -0.4302 -0.1284
+ 11SOL HW1 45 1.136 0.853 0.961 3.3277 0.8931 -1.0268
+ 11SOL HW2 46 1.134 0.710 0.911 -3.4316 -0.2829 1.5811
+ 12SOL OW 47 0.572 0.553 0.922 -0.1742 -0.7233 -0.1439
+ 12SOL HW1 48 0.490 0.597 0.942 -0.5892 -2.5031 2.8309
+ 12SOL HW2 49 0.546 0.464 0.897 0.6566 -2.2212 3.5366
+ 13SOL OW 50 0.723 1.509 0.511 -0.3090 0.4945 -0.3758
+ 13SOL HW1 51 0.746 1.596 0.543 -2.5021 0.5534 1.2725
+ 13SOL HW2 52 0.630 1.499 0.534 -0.3115 -1.9928 -1.1842
+ 14SOL OW 53 0.930 0.010 0.870 0.2867 -0.7696 0.3366
+ 14SOL HW1 54 1.010 0.062 0.862 0.1515 -0.7330 -0.8460
+ 14SOL HW2 55 0.909 -0.016 0.781 -0.8513 -1.0570 0.6778
+ 15SOL OW 56 0.812 1.183 0.926 -0.3575 -0.1102 0.2501
+ 15SOL HW1 57 0.831 1.091 0.946 0.5085 0.0415 0.1628
+ 15SOL HW2 58 0.740 1.180 0.863 -1.3766 -0.6744 1.3950
+ 16SOL OW 59 1.616 0.739 0.975 0.6902 -0.0641 -0.2024
+ 16SOL HW1 60 1.622 0.644 0.991 0.2136 0.1838 1.6857
+ 16SOL HW2 61 1.577 0.746 0.888 1.4594 -1.5956 -0.7170
+ 17SOL OW 62 0.867 1.731 0.604 0.0571 0.1554 0.0886
+ 17SOL HW1 63 0.885 1.797 0.537 2.4933 -0.8338 -0.3365
+ 17SOL HW2 64 0.953 1.696 0.627 -0.7371 0.0464 3.3598
+ 18SOL OW 65 0.317 1.465 1.113 0.0310 -0.6082 0.0339
+ 18SOL HW1 66 0.345 1.378 1.140 0.8547 -0.5831 -0.7124
+ 18SOL HW2 67 0.310 1.514 1.195 -0.0067 -1.2415 0.4180
+ 19SOL OW 68 0.710 1.130 1.294 -0.3148 -0.5390 0.6564
+ 19SOL HW1 69 0.763 1.073 1.351 -2.4262 -0.9910 2.2970
+ 19SOL HW2 70 0.764 1.208 1.282 1.2370 -1.4696 1.1918
+ 20SOL OW 71 1.790 0.577 0.171 -0.3471 0.3017 0.4965
+ 20SOL HW1 72 1.799 0.499 0.225 -0.9068 -0.6035 -0.6501
+ 20SOL HW2 73 1.699 0.575 0.141 -0.6113 1.8667 1.1189
+ 21SOL OW 74 1.308 0.199 1.101 -0.2490 0.0097 0.4805
+ 21SOL HW1 75 1.350 0.270 1.151 -0.3412 0.1916 0.2964
+ 21SOL HW2 76 1.357 0.121 1.126 -1.1832 -0.1423 1.9369
+ 22SOL OW 77 1.744 0.059 0.666 0.1375 -0.4188 -0.2149
+ 22SOL HW1 78 1.806 0.131 0.678 -1.1962 0.6080 0.8061
+ 22SOL HW2 79 1.739 0.046 0.571 0.0925 1.1353 -0.4502
+ 23SOL OW 80 0.901 0.770 1.809 -0.4861 -0.1675 0.1895
+ 23SOL HW1 81 0.956 0.838 1.770 -3.1820 2.4989 0.6603
+ 23SOL HW2 82 0.829 0.760 1.747 -1.5149 -0.5834 1.4163
+ 24SOL OW 83 1.431 0.095 0.816 -0.1274 -0.0072 -0.3712
+ 24SOL HW1 84 1.468 0.083 0.903 0.2089 1.8267 -0.2242
+ 24SOL HW2 85 1.506 0.088 0.757 0.7927 4.1506 -0.0367
+ 25SOL OW 86 1.780 1.754 0.862 0.5678 -0.1766 -0.1285
+ 25SOL HW1 87 1.744 1.827 0.811 2.8738 1.5084 0.4695
+ 25SOL HW2 88 1.779 1.786 0.952 -1.2405 -2.1875 0.6577
+ 26SOL OW 89 0.878 0.350 1.770 0.2313 -0.1715 -0.0881
+ 26SOL HW1 90 0.963 0.307 1.782 -0.7619 -1.8379 1.5806
+ 26SOL HW2 91 0.863 0.346 1.675 1.9075 0.0097 -0.3967
+ 27SOL OW 92 1.500 1.354 1.825 0.3244 -0.1483 0.2299
+ 27SOL HW1 93 1.464 1.401 1.900 0.7957 -0.9176 0.9363
+ 27SOL HW2 94 1.439 1.281 1.811 0.1258 0.1074 -0.2739
+ 28SOL OW 95 0.562 1.256 0.250 -0.1273 -0.1451 0.1098
+ 28SOL HW1 96 0.485 1.225 0.202 -0.4348 -0.3359 0.7185
+ 28SOL HW2 97 0.529 1.278 0.338 0.1864 1.3709 -0.1174
+ 29SOL OW 98 0.132 1.687 1.619 -0.0341 -0.1591 0.1320
+ 29SOL HW1 99 0.157 1.717 1.706 0.0736 0.6535 -0.1702
+ 29SOL HW2 100 0.177 1.747 1.559 -0.8985 -0.0896 -0.4585
+ 30SOL OW 101 0.760 1.304 0.060 0.9207 0.5245 0.1222
+ 30SOL HW1 102 0.676 1.293 0.105 0.0881 1.3490 -1.1581
+ 30SOL HW2 103 0.786 1.215 0.036 -0.7425 0.3888 -1.3994
+ 31SOL OW 104 0.536 1.614 0.108 0.4252 0.0036 0.1964
+ 31SOL HW1 105 0.500 1.696 0.074 -1.3980 -0.7305 0.2303
+ 31SOL HW2 106 0.602 1.642 0.171 0.8518 1.4200 -0.8172
+ 32SOL OW 107 0.057 0.491 0.440 0.2336 0.7963 -0.0595
+ 32SOL HW1 108 0.037 0.420 0.501 -1.7126 0.3097 -1.1592
+ 32SOL HW2 109 0.087 0.447 0.361 -0.6345 1.1979 -0.6241
+ 33SOL OW 110 1.490 1.658 1.513 -0.2644 -0.2673 -0.4947
+ 33SOL HW1 111 1.577 1.642 1.549 -1.3621 -1.1661 1.9584
+ 33SOL HW2 112 1.463 1.742 1.549 -1.5016 -1.3251 1.1927
+ 34SOL OW 113 0.782 1.561 1.523 -0.1664 0.0805 -0.4066
+ 34SOL HW1 114 0.723 1.563 1.448 -0.8568 -0.0627 0.1291
+ 34SOL HW2 115 0.745 1.494 1.581 0.6987 -0.2365 -0.2083
+ 35SOL OW 116 0.807 0.478 1.523 0.9213 -0.2462 0.2961
+ 35SOL HW1 117 0.820 0.485 1.429 0.8018 -0.9663 0.2173
+ 35SOL HW2 118 0.805 0.568 1.555 4.0443 0.0295 0.0500
+ 36SOL OW 119 1.587 1.228 1.226 -0.4386 -0.0224 -0.0371
+ 36SOL HW1 120 1.544 1.273 1.154 -0.8382 0.7052 0.6474
+ 36SOL HW2 121 1.628 1.297 1.277 -0.7828 -0.4496 0.8394
+ 37SOL OW 122 0.269 0.651 0.609 0.6461 -0.6178 -0.4651
+ 37SOL HW1 123 0.241 0.573 0.561 1.2497 -0.5481 -0.9303
+ 37SOL HW2 124 0.308 0.708 0.543 1.2428 -0.4092 0.0589
+ 38SOL OW 125 1.777 0.462 0.876 -0.1690 0.4649 -0.0234
+ 38SOL HW1 126 1.687 0.435 0.893 -0.0122 -1.9675 -2.4030
+ 38SOL HW2 127 1.829 0.416 0.942 -0.5391 0.7361 0.4603
+ 39SOL OW 128 1.128 0.090 1.778 -0.1059 1.0356 -0.1404
+ 39SOL HW1 129 1.077 0.112 1.700 -3.7084 0.5906 1.8990
+ 39SOL HW2 130 1.147 -0.004 1.768 -1.3247 0.7712 -0.1347
+ 40SOL OW 131 1.880 1.554 1.246 -0.2337 -0.2115 -0.5676
+ 40SOL HW1 132 1.816 1.510 1.303 -0.3159 0.0407 -0.4656
+ 40SOL HW2 133 1.941 1.485 1.221 -1.5338 -0.8466 -2.1069
+ 41SOL OW 134 0.573 0.170 0.681 -0.8153 0.6766 -0.6613
+ 41SOL HW1 135 0.627 0.199 0.608 0.6562 -0.0837 0.0758
+ 41SOL HW2 136 0.500 0.231 0.684 0.3922 2.1854 -1.2538
+ 42SOL OW 137 1.259 1.474 0.909 0.2779 -0.1363 0.3100
+ 42SOL HW1 138 1.167 1.464 0.883 -0.7646 1.7119 2.9065
+ 42SOL HW2 139 1.287 1.555 0.866 0.4561 -0.2780 0.1618
+ 43SOL OW 140 0.846 1.308 0.384 0.0963 -0.6847 -0.0161
+ 43SOL HW1 141 0.802 1.369 0.443 2.5698 0.1541 1.0892
+ 43SOL HW2 142 0.780 1.287 0.318 -2.1509 -0.0766 1.8855
+ 44SOL OW 143 1.165 1.684 0.100 0.2293 -0.2844 0.3432
+ 44SOL HW1 144 1.196 1.703 0.012 1.0789 -1.3255 0.4022
+ 44SOL HW2 145 1.084 1.635 0.088 -0.4374 0.8400 0.1710
+ 45SOL OW 146 0.773 0.931 0.338 0.2994 -0.1623 0.1571
+ 45SOL HW1 147 0.747 0.839 0.342 -1.6976 0.3519 0.3138
+ 45SOL HW2 148 0.726 0.972 0.410 0.9891 1.0238 -0.0469
+ 46SOL OW 149 0.211 1.744 1.089 -0.4382 0.0800 -0.1584
+ 46SOL HW1 150 0.155 1.667 1.082 -0.6996 0.3062 -0.5363
+ 46SOL HW2 151 0.266 1.741 1.011 0.7636 -0.6687 0.6860
+ 47SOL OW 152 0.850 0.577 1.284 0.0763 -0.1641 -0.5319
+ 47SOL HW1 153 0.867 0.606 1.194 -1.8434 1.1597 -0.5310
+ 47SOL HW2 154 0.756 0.559 1.285 -0.0726 0.5401 1.3774
+ 48SOL OW 155 1.736 0.661 1.369 -0.0923 0.0253 0.5089
+ 48SOL HW1 156 1.753 0.755 1.375 -0.1932 0.2521 -1.7129
+ 48SOL HW2 157 1.642 0.655 1.353 0.0258 -0.3834 -0.0572
+ 49SOL OW 158 1.726 0.997 1.222 0.6473 0.1426 0.3738
+ 49SOL HW1 159 1.736 0.982 1.128 1.7285 0.2828 0.4661
+ 49SOL HW2 160 1.674 1.078 1.228 1.8774 0.9978 -0.1221
+ 50SOL OW 161 0.337 1.867 1.542 -0.1395 0.0155 0.0325
+ 50SOL HW1 162 0.406 1.842 1.604 -0.0409 1.2725 0.4551
+ 50SOL HW2 163 0.376 1.854 1.456 0.3873 0.0639 0.2621
+ 51SOL OW 164 0.522 0.962 1.877 -0.1456 0.0945 -0.1389
+ 51SOL HW1 165 0.543 0.904 1.803 -1.8878 0.8212 -1.2614
+ 51SOL HW2 166 0.606 1.000 1.901 0.3613 0.6003 -2.4416
+ 52SOL OW 167 0.478 0.946 0.958 -0.7507 -0.1925 -0.3324
+ 52SOL HW1 168 0.433 0.923 0.877 -1.5686 -0.5832 0.2176
+ 52SOL HW2 169 0.414 0.999 1.006 -0.1425 0.3344 -0.0923
+ 53SOL OW 170 0.585 0.232 1.867 -0.2631 -0.2030 0.1275
+ 53SOL HW1 171 0.661 0.184 1.900 1.7167 1.6253 -1.4693
+ 53SOL HW2 172 0.552 0.179 1.795 0.8141 -0.0707 -0.4849
+ 54SOL OW 173 0.443 1.094 0.453 -0.6847 -0.4432 0.0280
+ 54SOL HW1 174 0.492 1.023 0.494 1.6368 0.4267 -1.1275
+ 54SOL HW2 175 0.352 1.079 0.482 0.2906 -1.7228 2.8010
+ 55SOL OW 176 0.103 1.416 0.916 0.6389 0.8565 -0.1103
+ 55SOL HW1 177 0.170 1.417 0.984 -0.4282 0.6462 0.9740
+ 55SOL HW2 178 0.113 1.331 0.873 0.4135 0.3871 0.7430
+ 56SOL OW 179 0.282 0.597 0.986 -0.5056 0.0759 -0.5233
+ 56SOL HW1 180 0.267 0.522 0.928 0.8633 0.8668 -1.9652
+ 56SOL HW2 181 0.246 0.672 0.939 -1.3875 0.4387 0.6785
+ 57SOL OW 182 1.519 0.738 0.725 0.5394 0.2421 -0.4307
+ 57SOL HW1 183 1.486 0.825 0.701 1.3444 0.5309 -0.4973
+ 57SOL HW2 184 1.475 0.678 0.665 0.5108 0.6770 -0.8445
+ 58SOL OW 185 1.203 0.280 1.483 0.5745 -0.4196 -0.2124
+ 58SOL HW1 186 1.131 0.221 1.504 1.7250 -1.9014 -0.2407
+ 58SOL HW2 187 1.165 0.346 1.425 -0.9650 -0.5636 0.5975
+ 59SOL OW 188 1.450 0.029 1.614 0.1531 -0.3262 -0.0153
+ 59SOL HW1 189 1.540 0.055 1.633 -0.3326 -0.4168 2.7153
+ 59SOL HW2 190 1.400 0.111 1.615 -0.1042 -0.4869 0.5555
+ 60SOL OW 191 0.331 1.467 -0.007 -0.4289 0.3722 0.2991
+ 60SOL HW1 192 0.405 1.526 0.008 -1.0610 1.1311 0.5110
+ 60SOL HW2 193 0.356 1.385 0.034 0.1041 0.7662 0.7662
+ 61SOL OW 194 1.280 0.843 0.558 -0.3066 -0.2319 0.2376
+ 61SOL HW1 195 1.230 0.866 0.480 -0.3337 -1.2591 -0.0616
+ 61SOL HW2 196 1.294 0.748 0.551 -0.4303 -0.3714 1.5404
+ 62SOL OW 197 1.873 1.232 0.298 -0.0038 0.7498 -0.2465
+ 62SOL HW1 198 1.853 1.139 0.291 2.5211 -0.0631 1.8894
+ 62SOL HW2 199 1.904 1.244 0.388 0.3511 3.5257 -0.6399
+ 63SOL OW 200 1.627 1.660 0.409 -0.4174 -0.0023 0.1415
+ 63SOL HW1 201 1.692 1.728 0.392 -0.3043 0.0330 0.7034
+ 63SOL HW2 202 1.632 1.602 0.333 -0.5729 0.6575 -0.3858
+ 64SOL OW 203 1.128 0.587 1.799 -0.5928 -0.4584 -0.0323
+ 64SOL HW1 204 1.078 0.664 1.828 -1.8369 -0.3563 -2.2123
+ 64SOL HW2 205 1.061 0.520 1.783 0.4115 -1.7925 1.0839
+ 65SOL OW 206 1.545 0.060 1.088 -0.5191 0.2959 -0.3816
+ 65SOL HW1 207 1.602 -0.013 1.110 -2.1657 -0.3298 2.3719
+ 65SOL HW2 208 1.576 0.132 1.144 -2.3760 -0.1021 1.2631
+ 66SOL OW 209 1.137 1.202 1.754 0.3946 0.5745 -0.1292
+ 66SOL HW1 210 1.089 1.283 1.737 -0.0973 0.4070 0.4246
+ 66SOL HW2 211 1.184 1.184 1.673 -1.5032 0.0345 -1.1792
+ 67SOL OW 212 0.172 1.278 0.592 0.7390 -0.5888 -0.2330
+ 67SOL HW1 213 0.104 1.211 0.584 -1.3115 1.0507 1.9439
+ 67SOL HW2 214 0.237 1.238 0.650 0.8866 -1.5993 -1.0619
+ 68SOL OW 215 0.091 1.384 1.778 0.0339 0.1204 -0.1674
+ 68SOL HW1 216 0.051 1.398 1.864 0.9592 -0.5806 0.3956
+ 68SOL HW2 217 0.173 1.433 1.781 0.2214 -0.1698 -0.5355
+ 69SOL OW 218 0.030 0.508 1.815 0.2233 -0.8501 -0.7350
+ 69SOL HW1 219 0.007 0.532 1.905 -1.2172 -1.6613 -0.8598
+ 69SOL HW2 220 0.110 0.457 1.824 0.6934 -0.0168 -0.0347
+ 70SOL OW 221 0.624 1.142 0.732 0.9632 -0.2790 0.2354
+ 70SOL HW1 222 0.650 1.062 0.686 1.2005 0.0460 -0.1941
+ 70SOL HW2 223 0.637 1.212 0.668 -0.3409 -0.0254 0.2101
+ 71SOL OW 224 1.193 1.767 0.601 -0.0623 -0.2111 -0.0925
+ 71SOL HW1 225 1.160 1.731 0.519 -0.7432 -2.9365 1.2332
+ 71SOL HW2 226 1.280 1.729 0.610 1.0328 2.0631 -0.6744
+ 72SOL OW 227 0.389 1.484 0.435 -0.0547 0.2064 0.2663
+ 72SOL HW1 228 0.337 1.405 0.448 0.7567 -0.1565 1.4080
+ 72SOL HW2 229 0.363 1.515 0.348 -1.9309 -0.1302 0.6606
+ 73SOL OW 230 0.781 1.678 0.205 -0.3629 -0.0256 -0.0008
+ 73SOL HW1 231 0.811 1.661 0.294 2.3232 -0.0677 -0.8296
+ 73SOL HW2 232 0.842 1.628 0.149 -0.6863 1.6180 -1.9228
+ 74SOL OW 233 1.055 0.474 1.005 0.4679 0.3957 0.3556
+ 74SOL HW1 234 1.021 0.386 1.022 0.5403 0.2219 -0.4039
+ 74SOL HW2 235 0.978 0.530 1.005 0.5974 0.6719 2.8347
+ 75SOL OW 236 0.312 1.722 0.841 0.4037 0.2797 0.0488
+ 75SOL HW1 237 0.402 1.692 0.826 0.4636 -0.7496 2.1319
+ 75SOL HW2 238 0.261 1.683 0.770 1.4923 0.4420 -0.8537
+ 76SOL OW 239 1.053 1.244 1.161 0.4135 0.1923 -0.4588
+ 76SOL HW1 240 1.109 1.313 1.195 1.6945 -0.9497 -0.1869
+ 76SOL HW2 241 1.047 1.261 1.067 -2.0376 2.5650 0.0064
+ 77SOL OW 242 0.988 1.507 1.679 -0.0500 0.3608 0.9478
+ 77SOL HW1 243 0.920 1.530 1.615 -0.6031 -0.6697 1.1496
+ 77SOL HW2 244 1.069 1.505 1.628 -0.7597 -2.5704 -0.2758
+ 78SOL OW 245 1.123 1.346 0.329 0.0394 -0.2192 -0.3380
+ 78SOL HW1 246 1.159 1.263 0.360 2.1408 1.1353 1.0555
+ 78SOL HW2 247 1.035 1.350 0.368 0.3071 -1.3402 0.4196
+ 79SOL OW 248 1.760 1.322 1.617 0.2581 -0.3836 0.2477
+ 79SOL HW1 249 1.708 1.258 1.666 0.3577 0.5835 1.6777
+ 79SOL HW2 250 1.839 1.335 1.669 -0.6782 2.4152 1.1537
+ 80SOL OW 251 1.425 1.061 0.668 0.0224 0.2524 -0.0414
+ 80SOL HW1 252 1.342 1.017 0.651 1.0290 -1.7478 -0.0527
+ 80SOL HW2 253 1.443 1.113 0.590 -2.4194 2.8859 0.9573
+ 81SOL OW 254 1.320 0.512 0.897 -0.4141 0.5363 0.5121
+ 81SOL HW1 255 1.232 0.475 0.884 0.0687 -0.2697 -0.6161
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+ 171SOL OW 524 1.627 0.342 1.494 0.1414 -0.1383 -0.7758
+ 171SOL HW1 525 1.667 0.414 1.541 -0.2790 0.9971 -2.0748
+ 171SOL HW2 526 1.687 0.268 1.506 1.3951 0.8610 -0.7125
+ 172SOL OW 527 0.599 0.001 1.650 0.3815 0.1828 0.0032
+ 172SOL HW1 528 0.680 -0.046 1.667 -0.5704 -1.4464 0.1983
+ 172SOL HW2 529 0.624 0.072 1.591 2.0275 0.0551 0.5107
+ 173SOL OW 530 0.829 0.629 1.019 -0.3081 0.1364 -0.5344
+ 173SOL HW1 531 0.756 0.579 0.983 -0.3983 0.2776 -0.5393
+ 173SOL HW2 532 0.799 0.719 1.021 -0.2808 0.1358 -0.1543
+ 174SOL OW 533 1.093 0.609 0.746 0.1080 -0.9383 0.2101
+ 174SOL HW1 534 1.179 0.600 0.705 -0.3239 -2.1067 -0.4914
+ 174SOL HW2 535 1.061 0.519 0.753 -1.1396 -0.4991 0.2711
+ 175SOL OW 536 0.382 0.669 0.181 -0.0411 -0.0296 -0.3837
+ 175SOL HW1 537 0.446 0.730 0.143 0.0147 0.4328 0.4324
+ 175SOL HW2 538 0.338 0.630 0.106 0.1336 0.8049 -0.9258
+ 176SOL OW 539 1.729 0.069 1.649 -0.1609 0.0338 -0.2796
+ 176SOL HW1 540 1.817 0.102 1.662 -0.2418 -0.0226 0.4400
+ 176SOL HW2 541 1.740 -0.011 1.598 0.1319 0.4733 -0.9063
+ 177SOL OW 542 1.033 0.269 0.315 -0.0583 0.5273 -0.2664
+ 177SOL HW1 543 1.039 0.192 0.258 -1.3009 0.6991 -0.6620
+ 177SOL HW2 544 1.102 0.255 0.381 -1.7250 -2.1534 1.1242
+ 178SOL OW 545 0.638 1.564 1.308 0.9879 0.3451 0.1004
+ 178SOL HW1 546 0.593 1.630 1.255 1.7351 -0.4089 -1.5325
+ 178SOL HW2 547 0.689 1.513 1.245 2.2259 -0.3480 1.6081
+ 179SOL OW 548 0.849 0.811 0.714 -0.3297 0.0631 -0.0330
+ 179SOL HW1 549 0.889 0.724 0.706 0.6064 0.4816 -0.0976
+ 179SOL HW2 550 0.918 0.865 0.754 -1.2964 0.5022 1.0885
+ 180SOL OW 551 0.247 0.144 0.323 0.7620 -0.1314 -0.5298
+ 180SOL HW1 552 0.339 0.117 0.329 0.7728 0.0771 0.4344
+ 180SOL HW2 553 0.203 0.094 0.392 0.7445 2.0063 1.1155
+ 181SOL OW 554 0.905 0.268 1.291 -0.1087 0.8316 -0.1332
+ 181SOL HW1 555 0.959 0.206 1.242 -0.3386 0.1706 0.4480
+ 181SOL HW2 556 0.968 0.327 1.332 0.1623 0.3640 0.1323
+ 182SOL OW 557 1.534 0.764 0.030 0.7388 -1.1581 -0.1142
+ 182SOL HW1 558 1.533 0.771 -0.065 -2.4562 0.4686 -0.0924
+ 182SOL HW2 559 1.467 0.698 0.049 -1.4724 1.2306 0.9793
+ 183SOL OW 560 1.111 1.088 0.132 0.0977 -0.1903 -0.3846
+ 183SOL HW1 561 1.118 1.130 0.047 1.2288 2.9893 1.1308
+ 183SOL HW2 562 1.018 1.091 0.154 0.2214 2.8112 0.1368
+ 184SOL OW 563 0.389 0.378 0.534 0.7580 0.1880 0.4997
+ 184SOL HW1 564 0.369 0.309 0.471 -0.1605 -0.0600 1.0385
+ 184SOL HW2 565 0.484 0.379 0.540 0.8041 -0.6119 0.0221
+ 185SOL OW 566 0.431 0.358 1.482 -0.4253 -0.2603 0.3808
+ 185SOL HW1 567 0.487 0.281 1.473 -0.0282 -0.0132 0.7159
+ 185SOL HW2 568 0.351 0.335 1.435 0.4819 -0.0953 -1.3014
+ 186SOL OW 569 0.794 1.018 0.077 -0.2885 -0.4398 -0.2982
+ 186SOL HW1 570 0.827 0.934 0.046 0.6657 -0.5674 0.9891
+ 186SOL HW2 571 0.774 1.004 0.169 1.2426 1.0816 0.3255
+ 187SOL OW 572 0.269 1.076 1.133 0.2871 -0.4073 0.2807
+ 187SOL HW1 573 0.317 1.147 1.176 0.9507 -1.1318 0.7502
+ 187SOL HW2 574 0.192 1.062 1.188 0.2100 -0.1254 0.2422
+ 188SOL OW 575 1.042 0.956 1.650 0.6219 0.5027 0.2090
+ 188SOL HW1 576 1.080 0.962 1.562 0.3210 0.1213 0.0520
+ 188SOL HW2 577 1.061 1.040 1.690 1.8995 0.2272 0.2379
+ 189SOL OW 578 1.824 1.106 0.552 -0.0312 0.2074 0.2984
+ 189SOL HW1 579 1.763 1.152 0.609 -1.9104 0.1423 -1.5645
+ 189SOL HW2 580 1.769 1.057 0.491 1.8783 -3.3129 1.1568
+ 190SOL OW 581 1.054 0.096 1.142 0.1424 0.1736 -0.0896
+ 190SOL HW1 582 1.145 0.123 1.155 0.8495 -0.7675 -2.6005
+ 190SOL HW2 583 1.059 0.006 1.111 -1.6094 0.2945 -0.8560
+ 191SOL OW 584 1.464 0.929 1.374 -0.7840 0.1841 -0.0787
+ 191SOL HW1 585 1.406 0.950 1.300 0.2915 0.0856 -0.9576
+ 191SOL HW2 586 1.548 0.968 1.350 -0.4300 0.1807 1.1218
+ 192SOL OW 587 0.012 0.300 0.632 -0.2338 0.3820 0.4414
+ 192SOL HW1 588 0.084 0.237 0.644 -0.2379 0.4817 1.0340
+ 192SOL HW2 589 -0.013 0.323 0.722 -1.2389 0.0768 0.2395
+ 193SOL OW 590 0.296 1.432 1.441 -0.2776 0.0987 0.4588
+ 193SOL HW1 591 0.352 1.484 1.499 -0.1029 1.4941 -0.9073
+ 193SOL HW2 592 0.229 1.395 1.499 -2.1585 4.1505 1.2038
+ 194SOL OW 593 1.724 0.222 1.223 -0.0971 -0.2705 0.3473
+ 194SOL HW1 594 1.805 0.238 1.174 -0.7701 -0.0003 -0.7339
+ 194SOL HW2 595 1.687 0.309 1.235 -0.4887 -0.4383 0.3465
+ 195SOL OW 596 0.239 0.128 1.156 -0.0509 0.0735 0.4442
+ 195SOL HW1 597 0.331 0.145 1.177 0.5986 -2.6979 0.1408
+ 195SOL HW2 598 0.235 0.034 1.139 -2.7258 0.3367 -0.7955
+ 196SOL OW 599 0.684 0.154 1.456 0.4064 -0.2548 0.6721
+ 196SOL HW1 600 0.694 0.070 1.410 -0.6471 1.1793 -2.4790
+ 196SOL HW2 601 0.740 0.214 1.407 -1.1448 1.4903 0.9542
+ 197SOL OW 602 1.495 0.941 0.224 -0.6476 0.1020 0.6122
+ 197SOL HW1 603 1.506 0.891 0.305 0.0679 -0.6466 0.0660
+ 197SOL HW2 604 1.518 0.880 0.155 2.1221 1.6765 -0.0041
+ 198SOL OW 605 1.036 0.044 0.155 0.3946 0.0169 0.6318
+ 198SOL HW1 606 1.075 0.066 0.070 -4.6592 -2.9339 -3.0146
+ 198SOL HW2 607 1.083 -0.034 0.183 1.6237 0.5698 0.1957
+ 199SOL OW 608 1.560 0.398 0.137 -0.2510 -0.3102 -0.5893
+ 199SOL HW1 609 1.517 0.457 0.075 0.2461 -1.2264 -1.8514
+ 199SOL HW2 610 1.571 0.316 0.089 1.5969 -0.5568 0.1623
+ 200SOL OW 611 0.970 0.122 1.559 0.2659 -0.0106 0.1344
+ 200SOL HW1 612 0.905 0.087 1.620 0.2449 -0.6184 -0.2425
+ 200SOL HW2 613 0.955 0.077 1.477 -0.3227 1.4846 -0.6213
+ 201SOL OW 614 0.039 0.512 1.167 -0.3820 0.4415 -0.1588
+ 201SOL HW1 615 -0.021 0.561 1.223 -1.3739 -1.4982 0.5836
+ 201SOL HW2 616 0.111 0.572 1.151 -2.0092 2.4944 -0.2107
+ 202SOL OW 617 1.207 0.684 1.504 0.1745 0.8391 0.2778
+ 202SOL HW1 618 1.178 0.669 1.594 1.4058 0.1195 0.5811
+ 202SOL HW2 619 1.150 0.629 1.451 1.0379 -0.6893 0.8803
+ 203SOL OW 620 0.104 0.130 1.637 0.3483 -0.1978 0.4295
+ 203SOL HW1 621 0.173 0.068 1.661 0.6514 -0.1759 -0.3658
+ 203SOL HW2 622 0.128 0.160 1.550 -1.4006 -1.2706 -0.4988
+ 204SOL OW 623 0.664 0.333 0.484 -0.5019 0.5074 -0.1531
+ 204SOL HW1 624 0.636 0.363 0.398 0.2203 -0.3359 -0.7075
+ 204SOL HW2 625 0.744 0.383 0.502 -0.9950 1.1307 0.3143
+ 205SOL OW 626 1.718 1.187 0.035 0.1019 -0.2635 0.1479
+ 205SOL HW1 627 1.700 1.281 0.036 1.5514 0.0948 -1.5510
+ 205SOL HW2 628 1.637 1.147 0.003 0.4417 0.7630 -2.1868
+ 206SOL OW 629 1.830 0.832 0.063 0.0241 -0.7700 -0.1381
+ 206SOL HW1 630 1.743 0.863 0.040 0.0302 -1.7006 -1.5835
+ 206SOL HW2 631 1.816 0.748 0.105 0.2634 -2.3400 -2.9703
+ 207SOL OW 632 1.013 1.355 0.890 -0.2500 0.2105 0.1626
+ 207SOL HW1 633 1.057 1.309 0.819 1.6440 -2.9574 3.0630
+ 207SOL HW2 634 0.934 1.304 0.908 0.4431 -0.3894 1.6704
+ 208SOL OW 635 1.407 0.307 1.672 0.1176 0.1925 -0.7822
+ 208SOL HW1 636 1.325 0.323 1.626 -0.5011 1.6870 0.7229
+ 208SOL HW2 637 1.475 0.336 1.611 -0.7356 3.5274 -0.3525
+ 209SOL OW 638 1.039 0.812 0.416 0.4649 -0.3159 0.6663
+ 209SOL HW1 639 0.962 0.813 0.359 1.5743 -0.9589 -0.9225
+ 209SOL HW2 640 1.029 0.734 0.470 -0.2237 -0.1281 0.8093
+ 210SOL OW 641 1.387 0.527 1.860 0.1367 -0.2000 0.3990
+ 210SOL HW1 642 1.305 0.564 1.828 0.5714 0.7206 0.3144
+ 210SOL HW2 643 1.411 0.461 1.795 0.6228 1.1183 -0.8116
+ 211SOL OW 644 1.707 0.257 0.342 -0.1176 -0.3400 0.3240
+ 211SOL HW1 645 1.670 0.314 0.274 -1.1406 -1.1743 0.1667
+ 211SOL HW2 646 1.771 0.312 0.387 -0.1592 0.5389 -0.6583
+ 212SOL OW 647 1.694 1.489 0.945 -0.0595 0.0324 0.2406
+ 212SOL HW1 648 1.709 1.578 0.914 0.9693 -0.7931 -1.7923
+ 212SOL HW2 649 1.782 1.450 0.950 -0.6292 -1.5645 -1.2353
+ 1.88572 1.88572 1.88572
diff --git a/test/gromacs/grompp.mdp b/test/gromacs/grompp.mdp
new file mode 100644
index 000000000..bc1aea719
--- /dev/null
+++ b/test/gromacs/grompp.mdp
@@ -0,0 +1,60 @@
+; Input file
+;
+define =
+; integrator
+integrator = md
+nsteps = 1000
+dt = 0.002
+;
+; removing CM translation and rotation
+comm_mode = Linear
+nstcomm = 1000
+;
+; output control
+nstlog = 100
+nstenergy = 10000
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; group definition
+nstxtcout = 10000
+xtc-precision = 10000
+xtc-grps = protein
+;
+; neighbour searching
+nstlist = 1
+ns_type = grid
+pbc = xyz
+rlist = 0.9
+;
+; electrostatic
+rcoulomb = 0.9
+coulombtype = pme
+fourierspacing = 0.12
+;
+; vdw
+vdw-type = Cut-off
+rvdw = 0.9
+;
+; constraints
+constraints = all-bonds
+constraint-algorithm = lincs
+lincs_iter = 4
+;
+; temperature
+Tcoupl = v-rescale
+tc_grps = system
+tau_t = 0.1
+ref_t = 300
+;
+; pression
+Pcoupl = Berendsen
+Pcoupltype = isotropic
+tau_p = 0.5
+compressibility = 4.5e-5
+ref_p = 1.0
+;
+; initial velocities
+gen_vel = yes
+gen_temp = 300
+gen_seed = 12334
diff --git a/test/gromacs/plumed.dat b/test/gromacs/plumed.dat
new file mode 100644
index 000000000..65ea3da71
--- /dev/null
+++ b/test/gromacs/plumed.dat
@@ -0,0 +1,33 @@
+LOAD ../../extensions/libplumedExtensions.dylib
+
+DISTANCE ATOMS=0,21 LABEL=C1 COMPONENTS
+VOLUME LABEL=vol
+ENERGY LABEL=ene
+
+COMBINE LABEL=x ARG=C1.x,C1.y,C1.z POWERS=2,2,2
+COMBINE LABEL=xx ARG=x POWERS=0.5
+
+#RESTRAINT ARG=C1 AT=1.1 KAPPA=10000.0
+
+#MOVINGRESTRAINT ARG=ene AT0=-8525.08 KAPPA0=0.024 AT1=-8000 STEP0=0 STEP1=10000
+#RESTRAINT ARG=ene AT=-8525.08 KAPPA=-0.0002 STRIDE=2
+
+RESTRAINT ARG=C1 AT=0.4 KAPPA=1000.0
+
+#RESTRAINT ARG=vol AT=6.8 KAPPA=100.0
+
+FLUSH STRIDE=100
+
+PRINT ARG=C1,vol,ene,C1.x,C1.y,C1.z STRIDE=1 FILE=COLVAR
+
+##PRINT ...
+## ARG=*.*
+## STRIDE=10
+## FILE=COLVAR_ALL
+##... PRINT
+
+DEBUG logActivity
+
+ENDPLUMED
+
+
diff --git a/test/gromacs/topol.top b/test/gromacs/topol.top
new file mode 100644
index 000000000..bd196c124
--- /dev/null
+++ b/test/gromacs/topol.top
@@ -0,0 +1,225 @@
+;
+; File 'topol.top' was generated
+; By user: max (559)
+; On host: ziggy.local
+; At date: Thu Feb 5 14:28:39 2009
+;
+; This is your topology file
+; "It's Calling Me to Break my Bonds, Again..." (Van der Graaf)
+;
+; Include forcefield parameters
+#include "ffoplsaa.itp"
+
+[ moleculetype ]
+; Name nrexcl
+Protein 3
+
+[ atoms ]
+; nr type resnr residue atom cgnr charge mass typeB chargeB massB
+ 1 opls_135 1 ACE CH3 1 -0.18 12.011 ; qtot -0.18
+ 2 opls_140 1 ACE HH31 1 0.06 1.008 ; qtot -0.12
+ 3 opls_140 1 ACE HH32 1 0.06 1.008 ; qtot -0.06
+ 4 opls_140 1 ACE HH33 1 0.06 1.008 ; qtot 0
+ 5 opls_235 1 ACE C 2 0.5 12.011 ; qtot 0.5
+ 6 opls_236 1 ACE O 2 -0.5 15.9994 ; qtot 0
+ 7 opls_238 2 ALA N 3 -0.5 14.0067 ; qtot -0.5
+ 8 opls_241 2 ALA H 3 0.3 1.008 ; qtot -0.2
+ 9 opls_224B 2 ALA CA 3 0.14 12.011 ; qtot -0.06
+ 10 opls_140 2 ALA HA 3 0.06 1.008 ; qtot 0
+ 11 opls_135 2 ALA CB 4 -0.18 12.011 ; qtot -0.18
+ 12 opls_140 2 ALA HB1 4 0.06 1.008 ; qtot -0.12
+ 13 opls_140 2 ALA HB2 4 0.06 1.008 ; qtot -0.06
+ 14 opls_140 2 ALA HB3 4 0.06 1.008 ; qtot 0
+ 15 opls_235 2 ALA C 5 0.5 12.011 ; qtot 0.5
+ 16 opls_236 2 ALA O 5 -0.5 15.9994 ; qtot 0
+ 17 opls_238 3 NAC N 6 -0.5 14.0067 ; qtot -0.5
+ 18 opls_241 3 NAC H 6 0.3 1.008 ; qtot -0.2
+ 19 opls_242 3 NAC CH3 7 0.02 12.011 ; qtot -0.18
+ 20 opls_140 3 NAC HH31 7 0.06 1.008 ; qtot -0.12
+ 21 opls_140 3 NAC HH32 7 0.06 1.008 ; qtot -0.06
+ 22 opls_140 3 NAC HH33 7 0.06 1.008 ; qtot 0
+
+[ bonds ]
+; ai aj funct c0 c1 c2 c3
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+ 5 6 1
+ 5 7 1
+ 7 8 1
+ 7 9 1
+ 9 10 1
+ 9 11 1
+ 9 15 1
+ 11 12 1
+ 11 13 1
+ 11 14 1
+ 15 16 1
+ 15 17 1
+ 17 18 1
+ 17 19 1
+ 19 20 1
+ 19 21 1
+ 19 22 1
+
+[ pairs ]
+; ai aj funct c0 c1 c2 c3
+ 1 8 1
+ 1 9 1
+ 2 6 1
+ 2 7 1
+ 3 6 1
+ 3 7 1
+ 4 6 1
+ 4 7 1
+ 5 10 1
+ 5 11 1
+ 5 15 1
+ 6 8 1
+ 6 9 1
+ 7 12 1
+ 7 13 1
+ 7 14 1
+ 7 16 1
+ 7 17 1
+ 8 10 1
+ 8 11 1
+ 8 15 1
+ 9 18 1
+ 9 19 1
+ 10 12 1
+ 10 13 1
+ 10 14 1
+ 10 16 1
+ 10 17 1
+ 11 16 1
+ 11 17 1
+ 12 15 1
+ 13 15 1
+ 14 15 1
+ 15 20 1
+ 15 21 1
+ 15 22 1
+ 16 18 1
+ 16 19 1
+ 18 20 1
+ 18 21 1
+ 18 22 1
+
+[ angles ]
+; ai aj ak funct c0 c1 c2 c3
+ 2 1 3 1
+ 2 1 4 1
+ 2 1 5 1
+ 3 1 4 1
+ 3 1 5 1
+ 4 1 5 1
+ 1 5 6 1
+ 1 5 7 1
+ 6 5 7 1
+ 5 7 8 1
+ 5 7 9 1
+ 8 7 9 1
+ 7 9 10 1
+ 7 9 11 1
+ 7 9 15 1
+ 10 9 11 1
+ 10 9 15 1
+ 11 9 15 1
+ 9 11 12 1
+ 9 11 13 1
+ 9 11 14 1
+ 12 11 13 1
+ 12 11 14 1
+ 13 11 14 1
+ 9 15 16 1
+ 9 15 17 1
+ 16 15 17 1
+ 15 17 18 1
+ 15 17 19 1
+ 18 17 19 1
+ 17 19 20 1
+ 17 19 21 1
+ 17 19 22 1
+ 20 19 21 1
+ 20 19 22 1
+ 21 19 22 1
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3 c4 c5
+ 2 1 5 6 3
+ 2 1 5 7 3
+ 3 1 5 6 3
+ 3 1 5 7 3
+ 4 1 5 6 3
+ 4 1 5 7 3
+ 1 5 7 8 3
+ 1 5 7 9 3
+ 6 5 7 8 3
+ 6 5 7 9 3
+ 5 7 9 10 3
+ 5 7 9 11 3
+ 5 7 9 15 3
+ 8 7 9 10 3
+ 8 7 9 11 3
+ 8 7 9 15 3
+ 7 9 11 12 3
+ 7 9 11 13 3
+ 7 9 11 14 3
+ 10 9 11 12 3
+ 10 9 11 13 3
+ 10 9 11 14 3
+ 15 9 11 12 3
+ 15 9 11 13 3
+ 15 9 11 14 3
+ 7 9 15 16 3
+ 7 9 15 17 3
+ 10 9 15 16 3
+ 10 9 15 17 3
+ 11 9 15 16 3
+ 11 9 15 17 3
+ 9 15 17 18 3
+ 9 15 17 19 3
+ 16 15 17 18 3
+ 16 15 17 19 3
+ 15 17 19 20 3
+ 15 17 19 21 3
+ 15 17 19 22 3
+ 18 17 19 20 3
+ 18 17 19 21 3
+ 18 17 19 22 3
+
+[ dihedrals ]
+; ai aj ak al funct c0 c1 c2 c3
+ 1 7 5 6 1 improper_O_C_X_Y
+ 5 9 7 8 1 improper_Z_N_X_Y
+ 9 17 15 16 1 improper_O_C_X_Y
+ 15 19 17 18 1 improper_Z_N_X_Y
+
+; Include Position restraint file
+#ifdef POSRES
+#include "posre.itp"
+#endif
+
+; Include water topology
+#include "tip3p.itp"
+
+#ifdef POSRES_WATER
+; Position restraint for each water oxygen
+[ position_restraints ]
+; i funct fcx fcy fcz
+ 1 1 1000 1000 1000
+#endif
+
+; Include generic topology for ions
+#include "ions.itp"
+
+[ system ]
+; Name
+Protein in water
+
+[ molecules ]
+; Compound #mols
+Protein 1
+SOL 209
diff --git a/test/link/.gitignore b/test/link/.gitignore
new file mode 100644
index 000000000..e9a57b6de
--- /dev/null
+++ b/test/link/.gitignore
@@ -0,0 +1,9 @@
+plumed
+plumed-static
+plumed-dummy
+plumedc
+plumedc-static
+plumedc-dummy
+plumedf
+plumedf-static
+plumedf-dummy
diff --git a/test/link/Makefile b/test/link/Makefile
new file mode 100644
index 000000000..6eb4d1806
--- /dev/null
+++ b/test/link/Makefile
@@ -0,0 +1,52 @@
+
+-include ../../Makefile.conf
+-include ../../src/Plumed.inc
+
+EXE=plumed plumedf plumedc \
+ plumed-static plumedf-static plumedc-static \
+ plumed-dummy plumedf-dummy plumedc-dummy
+
+all: $(EXE)
+
+plumed-dummy: main.o $(PLUMED_WRAPPER)
+ $(LD) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+plumed-static: main.o $(PLUMED_OBJ)
+ $(LD) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS) $(PLUMED_DYNAMIC_LIBS)
+
+plumed: main.o $(PLUMED_SHARED_OBJ)
+ $(LD) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+plumedf-dummy: mainf.o $(PLUMED_WRAPPER)
+ $(LDF90) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+plumedf-static: mainf.o $(PLUMED_OBJ)
+ $(LDF90) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS) $(PLUMED_DYNAMIC_LIBS)
+
+plumedf: mainf.o $(PLUMED_SHARED_OBJ)
+ $(LDF90) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+plumedc-dummy: mainc.o $(PLUMED_WRAPPER)
+ $(LD) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+plumedc-static: mainc.o $(PLUMED_OBJ)
+ $(LD) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS) $(PLUMED_DYNAMIC_LIBS)
+
+plumedc: mainc.o $(PLUMED_SHARED_OBJ)
+ $(LD) $(LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+clean:
+ rm -f *.o
+ rm -f $(EXE)
+ rm -f makefile.dep
+
+makefile.dep : *.c *.cpp *.h
+ for i in *.c *.cpp; do g++ $(CPPFLAGS) -MM "$${i}"; done > $@
+
+-include makefile.dep
+
+%.o : %.f90
+ $(FC) -c $(FFLAGS) $< -o $@
+
+
+
diff --git a/test/link/main.cpp b/test/link/main.cpp
new file mode 100644
index 000000000..bd591dc85
--- /dev/null
+++ b/test/link/main.cpp
@@ -0,0 +1,38 @@
+#include "Plumed.h"
+#include <cstdio>
+
+
+int ddoit(){
+ fprintf(stderr,"Callback\n");
+ return 10;
+}
+
+int main(int argc,char**argv){
+ PLMD::Plumed plumed;
+ bool inst=PLMD::installed();
+ char* input="plumed.dat";
+
+ if(argc>1 && argv[1]) input=argv[1];
+
+ if(inst){
+
+ int check;
+ plumed.cmd("checkAction DISTANCE",&check);
+ printf("Checking DISTANCE: %i\n",check);
+ plumed.cmd("checkAction DISTANCE1",&check);
+ printf("Checking DISTANCE1: %i\n",check);
+
+// {
+// plumed_function_holder xxx={(plumed_function_pointer)ddoit};
+// plumed.cmd("doit",&xxx);
+// }
+
+ plumed.cmd("setMDEngine","specific");
+ plumed.cmd("setLog",stdout);
+ int n=20;
+ plumed.cmd("setNatoms",&n);
+ plumed.cmd("setPlumedDat",input);
+ plumed.cmd("init");
+ }
+ return 0;
+}
diff --git a/test/link/mainc.c b/test/link/mainc.c
new file mode 100644
index 000000000..a7e035d81
--- /dev/null
+++ b/test/link/mainc.c
@@ -0,0 +1,25 @@
+#include "Plumed.h"
+#include <stdlib.h>
+
+int main(int argc,char** argv){
+ int check;
+ plumed p;
+ int natoms=3;
+
+ plumed_installed(&check);
+ if(check==1){
+ plumed_g_create();
+ plumed_g_cmd("setMDEngine","ACCode");
+ plumed_g_cmd("setNatoms",&natoms);
+ plumed_g_cmd("init",NULL);
+ plumed_g_cmd("read",NULL);
+ plumed_g_finalize();
+
+ p=plumed_create();
+ plumed_cmd(p,"setNatoms",&natoms);
+ plumed_cmd(p,"init",NULL);
+ plumed_cmd(p,"read",NULL);
+ plumed_finalize(p);
+ }
+ return 0;
+}
diff --git a/test/link/mainf.f90 b/test/link/mainf.f90
new file mode 100644
index 000000000..844856d52
--- /dev/null
+++ b/test/link/mainf.f90
@@ -0,0 +1,14 @@
+PROGRAM MAIN
+ IMPLICIT NONE
+ INTEGER :: check,natoms
+ natoms=5
+ CALL plumed_installed(check)
+ IF(check==1) THEN
+ CALL plumed_g_create()
+ CALL plumed_g_cmd("setMDEngine"//char(0),"AFortranCode"//char(0))
+ CALL plumed_g_cmd("setNatoms"//char(0),natoms)
+ CALL plumed_g_cmd("setPlumedDat"//char(0),"plumed.dat"//char(0))
+ CALL plumed_g_cmd("init"//char(0),0)
+ CALL plumed_g_finalize()
+ ENDIF
+END PROGRAM MAIN
diff --git a/test/link/plumed.dat b/test/link/plumed.dat
new file mode 100644
index 000000000..65c18c2e1
--- /dev/null
+++ b/test/link/plumed.dat
@@ -0,0 +1,4 @@
+DISTANCE LABEL=l1 ATOMS=0,1
+DISTANCE LABEL=l2 ATOMS=1,2
+PRINT
+PRINT
diff --git a/test/namd/.gitignore b/test/namd/.gitignore
new file mode 100644
index 000000000..eef64acc2
--- /dev/null
+++ b/test/namd/.gitignore
@@ -0,0 +1,7 @@
+*
+!namd_input
+!dia2.pdb
+!dia2.psf
+!plumed.dat
+!par_all27_prot_lipid.prm
+!.gitignore
diff --git a/test/namd/dia2.pdb b/test/namd/dia2.pdb
new file mode 100644
index 000000000..2ec141292
--- /dev/null
+++ b/test/namd/dia2.pdb
@@ -0,0 +1,24 @@
+REMARK original generated coordinate pdb file
+ATOM 1 C ALA 2 -0.186 -1.490 -0.181 1.00 0.00 DIA C
+ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 0.00 DIA O
+ATOM 3 NT ALA 2 0.008 -1.112 0.725 1.00 0.00 DIA N
+ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 0.00 DIA H
+ATOM 5 CAT ALA 2 -0.502 -1.632 1.410 1.00 0.00 DIA C
+ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 0.00 DIA H
+ATOM 7 HT2 ALA 2 -0.309 -1.255 2.315 1.00 0.00 DIA H
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 0.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 0.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 0.00 DIA H
+ATOM 11 HY2 ALA 2 -0.565 2.318 0.197 1.00 0.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 0.00 DIA H
+ATOM 13 CY ALA 2 -0.172 1.172 -0.892 1.00 0.00 DIA C
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 0.00 DIA O
+ATOM 15 N ALA 2 0.746 0.780 -0.955 1.00 0.00 DIA N
+ATOM 16 HN ALA 2 1.713 1.021 -0.873 1.00 0.00 DIA H
+ATOM 17 CA ALA 2 0.634 -0.654 -1.283 1.00 0.00 DIA C
+ATOM 18 HA ALA 2 0.099 -0.774 -2.218 1.00 0.00 DIA H
+ATOM 19 CB ALA 2 2.063 -1.223 -1.276 1.00 0.00 DIA C
+ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 0.00 DIA H
+ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 0.00 DIA H
+ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 0.00 DIA H
+END
diff --git a/test/namd/dia2.psf b/test/namd/dia2.psf
new file mode 100644
index 000000000..3f581d6d0
--- /dev/null
+++ b/test/namd/dia2.psf
@@ -0,0 +1,98 @@
+PSF
+
+ 6 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS 2 patches were applied to the molecule.
+ REMARKS topology top_all27_prot_lipid.rtf
+ REMARKS segment DIA { first ACE; last CT3; auto none }
+ REMARKS patch ACE DIA:2
+ REMARKS patch CT3 DIA:2
+
+ 22 !NATOM
+ 1 DIA 2 ALA C C 0.510000 12.0110 0
+ 2 DIA 2 ALA O O -0.510000 15.9990 0
+ 3 DIA 2 ALA NT NH1 -0.470000 14.0070 0
+ 4 DIA 2 ALA HNT H 0.310000 1.0080 0
+ 5 DIA 2 ALA CAT CT3 -0.110000 12.0110 0
+ 6 DIA 2 ALA HT1 HA 0.090000 1.0080 0
+ 7 DIA 2 ALA HT2 HA 0.090000 1.0080 0
+ 8 DIA 2 ALA HT3 HA 0.090000 1.0080 0
+ 9 DIA 2 ALA CAY CT3 -0.270000 12.0110 0
+ 10 DIA 2 ALA HY1 HA 0.090000 1.0080 0
+ 11 DIA 2 ALA HY2 HA 0.090000 1.0080 0
+ 12 DIA 2 ALA HY3 HA 0.090000 1.0080 0
+ 13 DIA 2 ALA CY C 0.510000 12.0110 0
+ 14 DIA 2 ALA OY O -0.510000 15.9990 0
+ 15 DIA 2 ALA N NH1 -0.470000 14.0070 0
+ 16 DIA 2 ALA HN H 0.310000 1.0080 0
+ 17 DIA 2 ALA CA CT1 0.070000 12.0110 0
+ 18 DIA 2 ALA HA HB 0.090000 1.0080 0
+ 19 DIA 2 ALA CB CT3 -0.270000 12.0110 0
+ 20 DIA 2 ALA HB1 HA 0.090000 1.0080 0
+ 21 DIA 2 ALA HB2 HA 0.090000 1.0080 0
+ 22 DIA 2 ALA HB3 HA 0.090000 1.0080 0
+
+ 21 !NBOND: bonds
+ 1 3 1 17 2 1 3 4
+ 3 5 5 6 5 7 5 8
+ 9 10 9 11 9 12 13 9
+ 13 15 14 13 15 16 15 17
+ 17 18 19 17 19 20 19 21
+ 19 22
+
+ 36 !NTHETA: angles
+ 1 17 18 1 3 5 1 3 4
+ 3 5 8 3 5 7 3 5 6
+ 3 1 2 3 1 17 4 3 5
+ 6 5 8 6 5 7 7 5 8
+ 9 13 14 9 13 15 10 9 12
+ 10 9 11 11 9 12 13 15 17
+ 13 15 16 13 9 12 13 9 11
+ 13 9 10 15 17 18 15 17 1
+ 15 13 14 16 15 17 17 19 22
+ 17 19 21 17 19 20 17 1 2
+ 19 17 18 19 17 1 19 17 15
+ 20 19 22 20 19 21 21 19 22
+
+ 41 !NPHI: dihedrals
+ 1 17 19 20 1 17 19 21
+ 1 17 19 22 1 17 15 13
+ 1 17 15 16 1 3 5 6
+ 1 3 5 7 1 3 5 8
+ 2 1 3 4 2 1 3 5
+ 2 1 17 19 2 1 17 15
+ 2 1 17 18 3 1 17 19
+ 3 1 17 15 3 1 17 18
+ 4 3 1 17 4 3 5 6
+ 4 3 5 7 4 3 5 8
+ 5 3 1 17 9 13 15 16
+ 9 13 15 17 10 9 13 15
+ 10 9 13 14 11 9 13 15
+ 11 9 13 14 12 9 13 15
+ 12 9 13 14 13 15 17 19
+ 13 15 17 18 14 13 15 16
+ 14 13 15 17 15 17 19 20
+ 15 17 19 21 15 17 19 22
+ 16 15 17 19 16 15 17 18
+ 18 17 19 20 18 17 19 21
+ 18 17 19 22
+
+ 4 !NIMPHI: impropers
+ 1 17 3 2 3 1 5 4
+ 13 9 15 14 15 13 17 16
+
+ 0 !NDON: donors
+
+
+ 0 !NACC: acceptors
+
+
+ 0 !NNB
+
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0
+
+ 1 0 !NGRP
+ 0 0 0
+
diff --git a/test/namd/namd_input b/test/namd/namd_input
new file mode 100644
index 000000000..3b4cd6ab5
--- /dev/null
+++ b/test/namd/namd_input
@@ -0,0 +1,43 @@
+# metadynamics
+
+plumed on
+plumedfile plumed.dat
+
+# set system
+structure ./dia2.psf
+coordinates ./dia2.pdb
+
+# ffield
+paratypecharmm on
+parameters ./par_all27_prot_lipid.prm
+exclude scaled1-4
+1-4scaling 1.0
+
+#approx
+switching on
+switchdist 20
+cutoff 22
+pairlistdist 22
+margin 0
+stepspercycle 1
+
+# integrator
+timestep 0.2
+
+#output
+outputenergies 1
+outputtiming 1
+binaryoutput no
+dcdfreq 10000
+outputname outconf
+
+# protocol
+temperature 300.0
+# Constant Temperature Control
+langevin on
+langevinDamping 5
+langevinTemp 300
+
+#script
+numsteps 1000
+seed 791064882
diff --git a/test/namd/par_all27_prot_lipid.prm b/test/namd/par_all27_prot_lipid.prm
new file mode 100755
index 000000000..025f4f378
--- /dev/null
+++ b/test/namd/par_all27_prot_lipid.prm
@@ -0,0 +1,3681 @@
+*>CHARMM22 All-Hydrogen Parameter File for Proteins and Lipids <<
+*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
+*>>>>>>>>>>>>>>>>>>>>>> July, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
+* All comments to ADM jr. via the CHARMM web site: www.charmm.org
+* parameter set discussion forum
+*
+
+! references
+!
+!PROTEINS
+!
+!MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the
+!treatment of backbone energetics in protein force fields: limitations
+!of gas-phase quantum mechanics in reproducing protein conformational
+!distributions in molecular dynamics simulations, Journal of
+!Computational Chemistry, 25: 1400-1415, 2004.
+!
+!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
+!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
+!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
+!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
+!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
+!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
+!empirical potential for molecular modeling and dynamics Studies of
+!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
+!
+!ZINC
+!
+!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
+!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
+!Structure, Function, and Genetics 23:12-31 (1995)
+!
+!LIPIDS
+!
+!Feller, S.E. Gawrisch, G. and MacKerell, Jr., A.D. Polyunsaturated
+!Fatty Acids in Lipid Bilayers: Intrinsic and Environmental
+!Contributions to Their Unique Physical Properties. Journal of
+!the American Chemical Society, 2002, 124:318-326
+!
+!Feller, S. and MacKerell, Jr., A.D. An Improved Empirical Potential
+!Energy Function for Molecular Simulations of Phospholipids, Journal
+!of Physical Chemistry B, 2000, 104: 7510-7515.
+!
+!and
+!
+!Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M.
+!Empirical Potential Energy Function for Phospholipids: Criteria for
+!Parameter Optimization and Applications, in "Biological Membranes: A
+!Molecular Perspective from Computation and Experiment," K.M. Merz and
+!B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.
+!
+!new ALKANES
+!
+!Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach
+!for the Optimization of Lennard-Jones Parameters. Journal of
+!Computational Chemistry, 1998, 19: 334-338.
+!
+!ALKENES
+!
+!Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D.,
+!Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration:
+!Parameterization and Comparison with Diffraction Studies. Biophysical
+!Journal, 73:2269-2279, 1997.
+!
+!new PHOSPHATE
+!
+!MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics
+!of Dimethylphosphate and its Implications For DNA Structure, Journal
+!de Chimie Physique, 1997, 94: 1436-1447.
+!
+!IONS
+!
+!all ions from Roux and coworkers
+!
+!Sodium
+!
+!Beglov, D. and Roux, B., Finite Representation of an Infinite
+!Bulk System: Solvent Boundary Potential for Computer Simulations,
+!Journal of Chemical Physics, 1994, 100: 9050-9063
+!
+
+BONDS
+!
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb b0
+!
+!Carbon Dioxide
+CST OST 937.96 1.1600 ! JES
+!Heme to Sulfate (PSUL) link
+SS FE 250.0 2.3200 !force constant a guess
+ !equilbrium bond length optimized to reproduce
+ !CSD survey values of
+ !2.341pm0.01 (mean, standard error)
+ !adm jr., 7/01
+C C 600.000 1.3350 ! ALLOW ARO HEM
+ ! Heme vinyl substituent (KK, from propene (JCS))
+CA CA 305.000 1.3750 ! ALLOW ARO
+ ! benzene, JES 8/25/89
+CE1 CE1 440.000 1.3400 !
+ ! for butene; from propene, yin/adm jr., 12/95
+CE1 CE2 500.000 1.3420 !
+ ! for propene, yin/adm jr., 12/95
+CE1 CT2 365.000 1.5020 !
+ ! for butene; from propene, yin/adm jr., 12/95
+CE1 CT3 383.000 1.5040 !
+ ! for butene, yin/adm jr., 12/95
+CE2 CE2 510.000 1.3300 !
+ ! for ethene, yin/adm jr., 12/95
+CP1 C 250.000 1.4900 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP1 CC 250.000 1.4900 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP1 CD 200.000 1.4900 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP1 222.500 1.5270 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP2 222.500 1.5370 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 CP2 222.500 1.5370 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CPB CE1 450.000 1.3800 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CPB CPA 299.800 1.4432 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPB CPB 340.700 1.3464 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPH1 CPH1 410.000 1.3600 ! ALLOW ARO
+ ! histidine, adm jr., 6/27/90
+CPM CPA 360.000 1.3716 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPT CA 305.000 1.3680 ! ALLOW ARO
+ ! adm jr., 12/30/91, for jwk
+CPT CPT 360.000 1.4000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
+ ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
+CT1 CC 200.000 1.5220 ! ALLOW POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT1 CD 200.000 1.5220 ! ALLOW POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT1 CT1 222.500 1.5000 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
+ ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
+CT2 CA 230.000 1.4900 ! ALLOW ALI ARO
+ ! phe,tyr, JES 8/25/89
+CT2 CC 200.000 1.5220 ! ALLOW POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT2 CD 200.000 1.5220 ! ALLOW POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT2 CPB 230.000 1.4900 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT2 CPH1 229.630 1.5000 ! ALLOW ARO
+ ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
+CT2 CT1 222.500 1.5380 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT2 CT2 222.500 1.5300 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO
+ ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91)
+CT3 CA 230.000 1.4900 ! ALLOW ALI ARO
+ ! toluene, adm jr. 3/7/92
+CT3 CC 200.000 1.5220 ! ALLOW POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT3 CD 200.000 1.5220 ! ALLOW POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT3 CPB 230.000 1.4900 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT3 CPH1 229.630 1.5000 ! ALLOW ARO
+ ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals
+CT3 CS 190.000 1.5310 ! ALLOW SUL
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+CT3 CT1 222.500 1.5380 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 CT2 222.500 1.5280 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 CT3 222.500 1.5300 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CY CA 350.000 1.3650 ! ALLOW ARO
+ !adm jr., 5/08/91, indole CCDB structure search
+CY CPT 350.000 1.4400 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CY CT2 230.000 1.5100 ! ALLOW ARO
+ !JWK Kb from alkane freq.. b0 from TRP crystal
+FE CM 258.000 1.9000 ! ALLOW HEM
+ ! Heme (6-liganded): CO ligand (KK 05/13/91)
+FE CPM 0.000 3.3814 ! ALLOW HEM
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
+H CD 330.000 1.1100 ! ALLOW PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+!HA C 330.000 1.1000 ! ALLOW ARO HEM
+ ! Heme vinyl substituent (KK, from propene (JCS))
+HA CA 340.000 1.0830 ! ALLOW ARO
+ ! trp, adm jr., 10/02/89
+HA CC 317.130 1.1000 ! ALLOW POL
+ ! adm jr., 5/13/91, formamide geometry and vibrations
+HA CP2 309.000 1.1110 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP3 309.000 1.1110 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CPM 367.600 1.0900 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+HA CS 300.000 1.1110 ! ALLOW SUL
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA CT1 309.000 1.1110 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT2 309.000 1.1110 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT3 322.000 1.1110 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CY 330.000 1.0800 ! ALLOW ARO
+ ! JWK 05/14/91 new r0 from indole
+HE1 CE1 360.500 1.1000 !
+ ! for propene, yin/adm jr., 12/95
+HE2 CE2 365.000 1.1000 !
+ ! for ethene, yin/adm jr., 12/95
+HB CP1 330.000 1.0800 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CT1 330.000 1.0800 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT2 330.000 1.0800 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT3 330.000 1.0800 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HP CA 340.000 1.0800 ! ALLOW ARO
+ ! phe,tyr JES 8/25/89
+HP CY 350.000 1.0800 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+HR1 CPH1 375.000 1.0830 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR1 CPH2 340.000 1.0900 ! ALLOW ARO
+ ! his, adm jr., 6/28/29
+HR2 CPH2 333.000 1.0700 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR3 CPH1 365.000 1.0830 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HT HT 0.000 1.5139 ! ALLOW WAT
+ ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM)
+N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP1 320.000 1.4340 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP3 320.000 1.4550 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO
+ ! 403.0->463.0, 1.305->1.365 guanidinium (KK)
+NC2 CT2 261.000 1.4900 ! ALLOW ALI POL
+ ! arg, (DS)
+NC2 CT3 261.000 1.4900 ! ALLOW ALI POL
+ ! methylguanidinium, adm jr., 3/26/92
+NC2 HC 455.000 1.0000 ! ALLOW POL
+ ! 405.0->455.0 GUANIDINIUM (KK)
+NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO
+ ! NMA Gas & Liquid Phase IR Spectra (LK)
+NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO
+ ! NMA Gas & Liquid Phase IR Spectra (LK)
+NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO
+ ! NMA Gas & Liquid Phase IR Spectra (LK)
+NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO
+ ! (DS)
+NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO
+ ! adm jr. 4/10/91, acetamide
+NH2 CT2 240.000 1.4550
+ ! from NH2 CT3, neutral glycine, adm jr.
+NH2 CT3 240.000 1.4550 ! ALLOW POL
+ ! methylamine geom/freq, adm jr., 6/2/92
+NH2 H 480.000 1.0000 ! ALLOW POL
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2 HC 460.000 1.0000 ! ALLOW POL
+ ! methylamine geom/freq, adm jr., 6/2/92
+NH3 CT1 200.000 1.4800 ! ALLOW ALI POL
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3 CT2 200.000 1.4800 ! ALLOW ALI POL
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3 CT3 200.000 1.4800 ! ALLOW ALI POL
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3 HC 403.000 1.0400 ! ALLOW POL
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+NP CP1 320.000 1.4850 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP3 320.000 1.5020 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP HC 460.000 1.0060 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NPH CPA 377.200 1.3757 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH FE 270.200 1.9580 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NR1 CPH1 400.000 1.3800 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR1 CPH2 400.000 1.3600 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR1 H 466.000 1.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH1 400.000 1.3800 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH2 400.000 1.3200 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 FE 65.000 2.2000 ! ALLOW HEM
+ ! Heme (6-liganded): His ligand (KK 05/13/91)
+NR3 CPH1 380.000 1.3700 ! ALLOW ARO
+ ! his, adm jr., 6/28/90
+NR3 CPH2 380.000 1.3200 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 H 453.000 1.0000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NY CA 270.000 1.3700 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+NY CPT 270.000 1.3750 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+NY H 465.000 0.9760 ! ALLOW ARO
+ ! indole JWK 08/28/89
+O C 620.000 1.2300 ! ALLOW PEP POL ARO
+ ! Peptide geometry, condensed phase (LK)
+O CC 650.000 1.2300 ! ALLOW PEP POL ARO
+ ! adm jr. 4/10/91, acetamide
+OB CC 750.000 1.2200 ! ALLOW PEP POL ARO
+ ! adm jr., 10/17/90, acetic acid vibrations and geom.
+OB CD 750.000 1.2200 ! ALLOW PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION
+ ! adm jr. 8/27/91, phenoxide
+OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION
+ ! adm jr. 7/23/91, acetic acid
+OC CT2 450.000 1.3300 ! ALLOW ALC
+ ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OC CT3 450.000 1.3300 ! ALLOW ALC
+ ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OH1 CA 334.300 1.4110 ! ALLOW ARO ALC
+ ! MeOH, EMB 10/10/89,
+OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC
+ ! adm jr. 5/02/91, acetic acid pure solvent
+OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO
+ ! methanol vib fit EMB 11/21/89
+OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO
+ ! methanol vib fit EMB 11/21/89
+OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO
+ ! methanol vib fit EMB 11/21/89
+OH1 H 545.000 0.9600 ! ALLOW ALC ARO
+ ! EMB 11/21/89 methanol vib fit
+OM CM 1115.000 1.1280 ! ALLOW HEM
+ ! Heme (6-liganded): CO ligand (KK 05/13/91)
+OM FE 250.000 1.8000 ! ALLOW HEM
+ ! Heme (6-liganded): O2 ligand (KK 05/13/91)
+OM OM 600.000 1.2300 ! ALLOW HEM
+ ! Heme (6-liganded): O2 ligand (KK 05/13/91)
+OS CD 150.000 1.3340 ! ALLOW POL PEP
+ ! adm jr. 5/02/91, acetic acid pure solvent
+OS CT3 340.000 1.4300 ! ALLOW POL PEP
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+OT HT 450.000 0.9572 ! ALLOW WAT
+ ! FROM TIPS3P GEOM
+S CT2 198.000 1.8180 ! ALLOW ALI SUL ION
+ ! fitted to C-S s 9/26/92 (FL)
+S CT3 240.000 1.8160 ! ALLOW ALI SUL ION
+ ! fitted to C-S s 9/26/92 (FL)
+S HS 275.000 1.3250 ! ALLOW SUL ION
+ ! methanethiol pure solvent, adm jr., 6/22/92
+SM CT2 214.000 1.8160 ! ALLOW SUL ION
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
+SM CT3 214.000 1.8160 ! ALLOW SUL ION
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
+SM SM 173.000 2.0290 ! ALLOW SUL ION
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
+SS CS 205.000 1.8360 ! ALLOW SUL
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+!lipid section
+CTL3 CL 200.0 1.522 ! methyl acetate
+CTL2 CL 200.0 1.522 ! methyl acetate
+CTL1 CL 200.0 1.522 ! methyl acetate
+OBL CL 750.0 1.220 ! methyl acetate
+OCL CL 525.0 1.260 ! acetate, protein
+OSL CL 150.0 1.334 ! methyl acetate
+OHL CL 230.0 1.40 ! methyl acetate
+HOL OHL 545.0 0.960 ! acetic acid
+CTL1 HAL1 309.00 1.111 ! alkanes, 3/92
+CTL2 HAL2 309.00 1.111 ! alkanes, 4/98
+CTL3 HAL3 322.00 1.111 ! alkanes, 4/98
+CTL3 OSL 340.0 1.43 ! phosphate
+CTL2 OSL 340.0 1.43 ! phosphate
+CTL1 OSL 340.0 1.43 ! phosphate
+OSL PL 270.0 1.60 ! phosphate
+O2L PL 580.0 1.48 ! phosphate
+OHL PL 237.0 1.59 ! phosphate
+NH3L HCL 410.0 1.04 ! ethanolamine
+NH3L CTL2 261.0 1.51 ! ethanolamine
+NTL CTL2 215.00 1.51 ! tetramethylammonium
+NTL CTL5 215.00 1.51 ! tetramethylammonium
+CTL5 HL 300.00 1.08 ! tetramethylammonium
+CTL2 HL 300.00 1.08 ! tetramethylammonium
+CTL1 CTL1 222.500 1.500 ! alkanes, 3/92
+CTL1 CTL2 222.500 1.538 ! alkanes, 3/92
+CTL1 CTL3 222.500 1.538 ! alkanes, 3/92
+CTL2 CTL2 222.500 1.530 ! alkanes, 3/92
+CTL2 CTL3 222.500 1.528 ! alkanes, 3/92
+CTL3 CTL3 222.500 1.530 ! alkanes, 3/92
+OHL CTL1 428.0 1.420 ! glycerol
+OHL CTL2 428.0 1.420 ! glycerol
+OHL CTL3 428.0 1.420 ! glycerol
+SL O2L 540.0 1.448 ! methylsulfate
+SL OSL 250.0 1.575 ! methylsulfate
+!HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)
+!HT OT 450.0 0.9572 ! from TIPS3P geometry
+CEL2 CEL2 510.000 1.330 ! ethene yin,adm jr., 12/95
+HEL2 CEL2 365.000 1.100 ! propene; from ethene, yin,adm jr., 12/95
+CEL1 CTL3 383.000 1.504 ! butene, yin,adm jr., 12/95
+CEL1 CEL2 500.000 1.342 ! propene, yin,adm jr., 12/95
+HEL1 CEL1 360.500 1.100 ! propene, yin,adm jr., 12/95
+CEL1 CTL2 365.000 1.502 ! butene; from propene, yin,adm jr., 12/95
+CEL1 CEL1 440.000 1.340 ! butene, yin,adm jr., 12/95
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!V(Urey-Bradley) = Kub(S - S0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!Kub: kcal/mole/A**2 (Urey-Bradley)
+!S0: A
+!
+!atom types Ktheta Theta0 Kub S0
+!
+!Carbon Dioxide, JES
+OST CST OST 3000.00 180.0000 ! CO2, JES
+!Heme to Sulfate (PSUL) link
+CS SS FE 50.0 100.6 !force constant a guess
+ !equilibrium angle optimized to reproduce
+ !CSD survey values
+ !107.5pm0.6 (mean, standard error)
+ !adm jr., 7/01
+SS FE NPH 100.0 90.0 !force constant a guess
+ !adm jr., 7/01
+!
+CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO
+ ! JES 8/25/89
+CE1 CE1 CT2 48.00 123.50 !
+ ! for 2-butene, yin/adm jr., 12/95
+CE1 CE1 CT3 48.00 123.50 !
+ ! for 2-butene, yin/adm jr., 12/95
+CE1 CT2 CT3 32.00 112.20 !
+ ! for 1-butene; from propene, yin/adm jr., 12/95
+CE2 CE1 CT2 48.00 126.00 !
+ ! for 1-butene; from propene, yin/adm jr., 12/95
+CE2 CE1 CT3 47.00 125.20 !
+ ! for propene, yin/adm jr., 12/95
+CP1 N C 60.000 117.0000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP1 C 52.000 112.3000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 N C 60.000 117.0000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 N CP1 100.000 114.2000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 NP CP1 100.000 111.0000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CPA CPB CE1 70.000 126.7400 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CPA CPM CPA 94.200 125.1200 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPA NPH CPA 139.300 103.9000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPB CE1 CE2 70.000 121.5000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CPB CPB CE1 70.000 126.7500 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CPB CPB CPA 30.800 106.5100 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+CPM CPA CPB 61.600 124.0700 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPT CA CA 60.000 118.0000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CPT CPT CA 60.000 122.0000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CPT NY CA 110.000 108.0000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
+ ! PARALLH19 (JES)
+CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
+CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
+ ! alkane frequencies (MJF), alkane geometries (SF)
+CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
+ ! NMA Vib Modes (LK)
+CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO
+ ! PARALLH19 (JES)
+CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
+CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! from CT2 CT1 C, for lactams, adm jr.
+CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
+ ! alkane frequencies (MJF), alkane geometries (SF)
+CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
+ ! alkane frequencies (MJF), alkane geometries (SF)
+CT2 CY CA 45.800 129.4000 ! ALLOW ARO
+ !adm jr., 5/08/91, indole CCDB structure search
+CT2 CY CPT 45.800 124.0000 ! ALLOW ARO
+ !adm jr., 5/08/91, indole CCDB structure search
+CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
+ ! 107.5->120.0 to make planar Arg (KK)
+CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
+ ! NMA Vib Modes (LK)
+CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO
+ ! toluene, adm jr., 3/7/92
+CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS
+CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/09/92, for ALA cter
+CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO
+ ! ethylbenzene, adm jr., 3/7/92
+CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted
+CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI
+ ! alkane frequencies (MJF), alkane geometries (SF)
+CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO
+ ! methylguanidinium, adm jr., 3/26/92
+CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO
+ ! NMA Vib Modes (LK)
+CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP
+ ! adm jr. 5/02/91, acetic acid pure solvent
+CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION
+ ! expt. MeEtS, 3/26/92 (FL)
+CY CPT CA 160.000 130.6000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CY CPT CPT 110.000 107.4000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+CY CT2 CT1 58.350 114.0000 ! ALLOW ARO
+ ! from TRP crystal, JWK
+CY CT2 CT3 58.350 114.0000 ! ALLOW ARO
+ ! from TRP crystal, JWK
+FE NPH CPA 96.150 128.0500 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO
+ ! NMA Vib Modes (LK)
+H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI
+ ! NMA Vibrational Modes (LK)
+H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI
+ ! NMA Vibrational Modes (LK)
+H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI
+ ! NMA Vibrational Modes (LK)
+H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO
+ ! his, adm jr. 8/13/90 acetamide geometry and vibrations
+H NH2 H 23.000 120.0000 ! ALLOW POL
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
+H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+H NY CA 28.000 126.0000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+H NY CPT 28.000 126.0000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO
+ ! JES 8/25/89 phenol
+H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI
+ ! methanol vib fit EMB 11/21/89
+H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI
+ ! methanol vib fit EMB 11/21/89
+H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI
+ ! methanol vib fit EMB 11/21/89
+!HA C C 50.000 120.5000 ! ALLOW PEP POL ARO
+ ! Heme vinyl substituent (KK from propene (JCS))
+!HA C CPB 50.000 120.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+!HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO
+ ! Heme vinyl substituent (KK from propene (JCS))
+HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO
+ ! trp, adm jr., 10/02/89
+HA CA CPT 41.000 122.0000 ! ALLOW ARO
+ !adm jr., 5/08/91, indole CCDB structure search
+HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
+ ! JWK 05/14/91 new theta0 and r0UB from indole
+HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CPM CPA 12.700 117.4400 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+HA CPM FE 0.000 180.0000 ! ALLOW HEM
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
+HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
+HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd
+ ! based on HA CT2 HA
+HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
+HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO
+ ! PARALLH19 (JES)
+HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+HA CT2 CE1 45.00 111.50 !
+ ! for 1-butene; from propene, yin/adm jr., 12/95
+HA CT2 CPB 50.000 109.5000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
+HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane frequencies (MJF), alkane geometries (SF)
+HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT2 CY 33.430 109.5000 ! ALLOW ARO
+ ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA
+HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! alanine dipeptide, LK, replaced, adm jr., 5/09/91
+HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO
+ ! toluene, adm jr. 3/7/92
+HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+HA CT3 CE1 42.00 111.50 !
+ ! for 2-butene, yin/adm jr., 12/95
+HA CT3 CPB 50.000 109.5000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED
+HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane frequencies (MJF), alkane geometries (SF)
+HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO
+ ! JWK 05/14/91 new theta0 and r0UB from indole
+HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
+ ! JWK 05/14/91 new theta0 and r0UB from indole
+HE1 CE1 CE1 52.00 119.50 !
+ ! for 2-butene, yin/adm jr., 12/95
+HE1 CE1 CE2 42.00 118.00 !
+ ! for propene, yin/adm jr., 12/95
+HE1 CE1 CT2 40.00 116.00 !
+ ! for 1-butene; from propene, yin/adm jr., 12/95
+HE1 CE1 CT3 22.00 117.00 !
+ ! for propene, yin/adm jr., 12/95
+HE1 CE1 CPB 50.000 120.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+HE2 CE2 CE1 45.00 120.50 !
+ ! for propene, yin/adm jr., 12/95
+HE2 CE2 CE2 55.50 120.50 !
+ ! for ethene, yin/adm jr., 12/95
+HE2 CE2 HE2 19.00 119.00 !
+ ! for propene, yin/adm jr., 12/95
+HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CT1 C 50.000 109.5000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+HB CT1 CT1 35.000 111.0000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT1 CT2 35.000 111.0000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT1 CT3 35.000 111.0000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT2 C 50.000 109.5000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+HB CT2 HB 36.000 115.0000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT3 C 50.000 109.5000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO
+ ! 35.3->49.0 GUANIDINIUM (KK)
+HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI
+ ! 107.5->120.0 to make planar Arg (KK)
+HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI
+ ! methylguanidinium, adm jr., 3/26/92
+HC NC2 HC 25.000 120.0000 ! ALLOW POL
+ ! 40.0->25.0 GUANIDINIUM (KK)
+HC NH2 CT2 50.000 111.0000 ! ALLOW POL
+ ! from HC NH2 CT3, neutral glycine, adm jr.
+HC NH2 CT3 50.000 111.0000 ! ALLOW POL
+ ! methylamine geom/freq, adm jr., 6/2/92
+HC NH2 HC 39.000 106.5000 ! ALLOW POL
+ ! 40.0->25.0 GUANIDINIUM (KK)
+HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+HC NH3 HC 44.000 109.5000 ! ALLOW POL
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP HC 51.000 107.5000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO
+ ! JES 8/25/89 benzene
+HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO
+ ! JWK 05/14/91 new theta0 and r0UB from indole
+HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO
+ ! JWK 05/14/91 new theta0 and r0UB from indole
+HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO
+ ! adm jr., 6/27/90, his
+HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HT OT HT 55.000 104.5200 ! ALLOW WAT
+ ! TIP3P GEOMETRY, ADM JR.
+N C CP1 20.000 112.5000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP1 C 50.000 108.2000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP1 CC 50.000 108.2000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP1 CP2 70.000 110.8000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP3 CP2 70.000 110.5000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO
+ ! changed from 60.0/120.3 for guanidinium (KK)
+NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL
+ ! arg, (DS)
+NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL
+ ! arg, (DS)
+NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL
+ ! methylguanidinium, adm jr., 3/26/92
+NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO
+ ! NMA Vib Modes (LK)
+NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO
+ ! NMA Vib Modes (LK)
+NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO
+ ! NMA Vib Modes (LK)
+NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
+ ! adm jr. 5/02/91, acetic acid pure solvent
+NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI
+ ! adm jr. 5/20/92, for asn,asp,gln,glu and cters
+NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI
+ ! adm jr. 5/02/91, acetic acid pure solvent
+NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO
+ ! from NH1 CT1 CT2, for lactams, adm jr.
+NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
+ ! from NH1 CT3 HA, for lactams, adm jr.
+NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO
+ ! NMA crystal (JCS)
+NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 8/13/90 acetamide geometry and vibrations
+NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL
+ ! adm jr., 5/13/91, formamide geometry and vibrations
+NH2 CT2 HA 38.000 109.50 50.00 2.14000
+ !from NH2 CT3 HA, neutral lysine
+NH2 CT2 HB 38.000 109.50 50.00 2.14000
+ !from NH2 CT3 HA, neutral glycine, adm jr.
+NH2 CT2 CD 52.000 108.0000
+ !from CT2 CT2 CD, neutral glycine, adm jr.
+NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
+ !from NH3 CT2 CT2, neutral lysine
+NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL
+ ! methylamine geom/freq, adm jr., 6/2/92
+NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
+ ! new aliphatics, adm jr., 2/3/92
+NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL
+ ! new aliphatics, adm jr., 2/3/92
+NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL
+ ! new aliphatics, adm jr., 2/3/92
+NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL
+ ! new aliphatics, adm jr., 2/3/92
+NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP
+ ! new aliphatics, adm jr., 2/3/92
+NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI
+ ! alanine (JCS)
+NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI
+ ! adm jr. 5/02/91, acetic acid pure solvent
+NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL
+ ! alanine (JCS)
+NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP
+ ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK)
+NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL
+ ! new stretch and bend; methylammonium (KK 03/10/92)
+NP CP1 C 50.000 106.0000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 CC 50.000 106.0000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 CP2 70.000 108.5000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP3 CP2 70.000 108.5000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NPH CPA CPB 122.000 111.5400 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH CPA CPM 88.000 124.3900 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH FE CM 50.000 90.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+NPH FE CPM 0.000 45.0000 ! ALLOW HEM
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
+NPH FE NPH 14.390 90.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR2 FE CM 50.000 180.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+NR2 FE NPH 50.000 90.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FC FROM CA CT2CT
+NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO
+ ! JWK 05/14/91 new theta0 and r0UB from indole
+NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO
+ ! JWK 05/14/91 new theta0 and r0UB from indole
+NY CPT CA 160.000 130.6000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+NY CPT CPT 110.000 107.4000 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+O C CP1 80.000 118.0000 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C H 50.000 121.7000 ! ALLOW PEP POL ARO
+ ! acetaldehyde (JCS)
+O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO
+ ! NMA Vib Modes (LK)
+O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/10/91, acetamide update
+O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/10/91, acetamide update
+O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 4/10/91, acetamide update
+O CC HA 44.000 122.0000 ! ALLOW POL
+ ! adm jr., 5/13/91, formamide geometry and vibrations
+O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO
+ ! adm jr. 4/10/91, acetamide update
+OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO
+ ! adm jr. 5/02/91, acetic acid pure solvent
+OC CA CA 40.000 120.0000 ! ALLOW POL ARO
+ ! adm jr. 8/27/91, phenoxide
+OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO
+ ! adm jr. 7/23/91, correction, ACETATE (KK)
+OC CT2 CT3 65.000 122.0000 ! ALLOW ALC
+ ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OC CT2 HA 65.000 118.3000 ! ALLOW ALC
+ ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OC CT3 HA 65.000 118.3000 ! ALLOW ALC
+ ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92
+OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC
+ ! PARALLH19 WITH [122.3] (JES)
+OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
+ ! adm jr, 10/17/90, acetic acid vibrations
+OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC
+ ! adm jr, 10/17/90, acetic acid vibrations
+OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC
+ ! adm jr, 10/17/90, acetic acid vibrations
+OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO
+ ! MeOH, EMB, 10/10/89
+OM CM FE 35.000 180.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+OM FE NPH 5.000 90.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+OM OM FE 0.000 180.0000 ! ALLOW HEM
+ ! Heme (6-liganded): ligand links (KK 05/13/91)
+OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP
+ ! adm jr., 4/05/91, for PRES CT1 from methylacetate
+OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL
+ ! adm jr. 4/05/91, for PRES CT1 from methyl acetate
+OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL
+ ! adm jr. 4/05/91, for PRES CT1 from methyl acetate
+S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
+ ! as in expt.MeEtS & DALC crystal, 5/15/92
+S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION
+ ! expt. MeEtS, 3/26/92 (FL)
+S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION
+ ! expt. MeEtS, 3/26/92 (FL)
+S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION
+ ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
+S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION
+ ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90
+SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION
+ ! as in expt.MeEtS & DALC crystal, 5/15/92
+SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION
+ ! new S-S atom type 8/24/90
+SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION
+ ! new S-S atom type 8/24/90
+SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
+SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
+SS CS CT3 55.000 118.0000 ! ALLOW SUL
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+SS CS HA 40.000 112.3000 ! ALLOW SUL
+ ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+!lipid section
+OBL CL CTL3 70.0 125.0 20.0 2.442 ! methyl acetate
+OBL CL CTL2 70.0 125.0 20.0 2.442 ! methyl acetate
+OBL CL CTL1 70.0 125.0 20.0 2.442 ! methyl acetate
+OSL CL OBL 90.0 125.9 160.0 2.2576 ! acetic acid
+CL OSL CTL1 40.0 109.6 30.0 2.2651 ! methyl acetate
+CL OSL CTL2 40.0 109.6 30.0 2.2651 ! methyl acetate
+CL OSL CTL3 40.0 109.6 30.0 2.2651 ! methyl acetate
+HAL2 CTL2 CL 33.00 109.50 30.00 2.163 ! methyl acetate
+HAL3 CTL3 CL 33.00 109.50 30.00 2.163 ! methyl acetate
+CTL2 CTL2 CL 52.0 108.00 ! alkane
+CTL3 CTL2 CL 52.0 108.00 ! alkane
+OSL CL CTL3 55.0 109.0 20.00 2.3260 ! methyl acetate
+OSL CL CTL2 55.0 109.0 20.00 2.3260 ! methyl acetate
+OHL CL OBL 50.0 123.0 210.0 2.2620 ! acetic acid
+OCL CL CTL2 40.0 118.0 50.0 2.3880 ! acetate
+OCL CL CTL3 40.0 118.0 50.0 2.3880 ! acetate
+OCL CL OCL 100.0 124.0 70.0 2.2250 ! acetate
+OHL CL CTL3 55.0 110.50 ! acetic acid
+OHL CL CTL2 55.0 110.50 ! acetic acid
+HOL OHL CL 55.0 115.0 ! acetic acid
+OSL CTL1 CTL2 75.700 110.10 ! acetic acid
+OSL CTL1 CTL3 75.700 110.10 ! acetic acid
+OSL CTL2 CTL1 75.700 110.10 ! acetic acid
+OSL CTL2 CTL2 75.700 110.10 ! acetic acid
+OSL CTL2 CTL3 75.700 110.10 ! acetic acid
+HAL2 CTL2 HAL2 35.500 109.00 5.40 1.80200 ! alkane, 3/92
+HAL3 CTL3 HAL3 35.500 108.40 5.40 1.80200 ! alkane, 3/92
+HAL1 CTL1 OSL 60.0 109.5 ! phosphate
+HAL2 CTL2 OSL 60.0 109.5 ! phosphate
+HAL3 CTL3 OSL 60.0 109.5 ! phosphate
+CTL2 OSL PL 20.0 120.0 35.0 2.33 ! phosphate
+CTL3 OSL PL 20.0 120.0 35.0 2.33 ! phosphate
+HOL OHL PL 30.0 115.0 40.0 2.30 ! phosphate
+OSL PL OSL 80.0 104.3 ! phosphate
+OSL PL O2L 98.9 111.6 ! phosphate
+OSL PL OHL 48.1 108.0 ! phosphate
+O2L PL O2L 120.0 120.0 ! phosphate
+O2L PL OHL 98.9 108.23 ! phosphate
+NTL CTL2 HL 40.0 109.5 27. 2.13 ! tetramethylammonium
+NTL CTL5 HL 40.0 109.5 27. 2.13 ! tetramethylammonium
+HL CTL2 HL 24.0 109.50 28. 1.767 ! tetramethylammonium
+HL CTL5 HL 24.0 109.50 28. 1.767 ! tetramethylammonium
+CTL2 NTL CTL2 60.0 109.5 26. 2.466 ! tetraethylammonium, from CTL5 NTL CTL2
+CTL5 NTL CTL2 60.0 109.5 26. 2.466 ! tetramethylammonium
+CTL5 NTL CTL5 60.0 109.5 26. 2.466 ! tetramethylammonium
+HL CTL2 CTL2 33.430 110.10 22.53 2.179 ! alkane
+HL CTL2 CTL3 33.430 110.10 22.53 2.179 ! alkane
+HAL1 CTL1 CTL1 34.500 110.10 22.53 2.179 ! alkane, 3/92
+HAL1 CTL1 CTL2 34.500 110.10 22.53 2.179 ! alkane, 3/92
+HAL1 CTL1 CTL3 34.500 110.10 22.53 2.179 ! alkane, 3/92
+HAL2 CTL2 CTL1 26.500 110.10 22.53 2.179 ! alkane, 4/98
+HAL2 CTL2 CTL2 26.500 110.10 22.53 2.179 ! alkane, 4/98
+HAL2 CTL2 CTL3 34.600 110.10 22.53 2.179 ! alkane, 4/98
+HAL3 CTL3 CTL1 33.430 110.10 22.53 2.179 ! alkane, 4/98
+HAL3 CTL3 CTL2 34.600 110.10 22.53 2.179 ! alkane, 4/98
+HAL3 CTL3 CTL3 37.500 110.10 22.53 2.179 ! alkane, 4/98
+NTL CTL2 CTL2 67.7 115.00 ! tetramethylammonium
+NTL CTL2 CTL3 67.7 115.00 ! tetramethylammonium
+HCL NH3L CTL2 33.0 109.50 4.00 2.056 ! ethanolamine
+HCL NH3L HCL 41.0 109.50 ! ethanolamine
+NH3L CTL2 CTL2 67.7 110.00 ! ethanolamine
+NH3L CTL2 HAL2 45.0 107.50 35.00 2.0836 ! ethanolamine
+CTL1 CTL1 CTL1 53.350 111.00 8.00 2.561 ! alkane, 3/92
+CTL1 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol
+CTL1 CTL1 CTL3 53.350 108.50 8.00 2.561 ! alkane, 3/92
+CTL1 CTL2 CTL1 58.350 113.50 11.16 2.561 ! glycerol
+CTL1 CTL2 CTL2 58.350 113.50 11.16 2.561 ! glycerol
+CTL1 CTL2 CTL3 58.350 113.50 11.16 2.561 ! glycerol
+CTL2 CTL1 CTL2 58.350 113.50 11.16 2.561 ! glycerol
+CTL2 CTL1 CTL3 58.350 113.50 11.16 2.561 ! glycerol
+CTL2 CTL2 CTL2 58.350 113.60 11.16 2.561 ! alkane, 3/92
+CTL2 CTL2 CTL3 58.000 115.00 8.00 2.561 ! alkane, 3/92
+HOL OHL CTL1 57.500 106.00 ! glycerol
+HOL OHL CTL2 57.500 106.00 ! glycerol
+HOL OHL CTL3 57.500 106.00 ! glycerol
+OHL CTL1 CTL2 75.700 110.10 ! glycerol
+OHL CTL2 CTL1 75.700 110.10 ! glycerol
+OHL CTL2 CTL2 75.700 110.10 ! glycerol
+OHL CTL2 CTL3 75.700 110.10 ! glycerol
+OHL CTL1 HAL1 45.900 108.89 ! glycerol
+OHL CTL2 HAL2 45.900 108.89 ! glycerol
+OHL CTL3 HAL3 45.900 108.89 ! glycerol
+O2L SL O2L 130.0 109.47 35.0 2.45 ! methylsulfate
+O2L SL OSL 85.0 98.0 ! methylsulfate
+CTL2 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate
+CTL3 OSL SL 15.0 109.0 27.00 1.90 ! methylsulfate
+!HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY
+CEL1 CEL1 CTL2 48.00 123.50 ! from 2-butene, yin,adm jr., 12/95
+CEL1 CEL1 CTL3 48.00 123.50 ! 2-butene, yin,adm jr., 12/95
+CEL2 CEL1 CTL2 48.00 126.00 ! 1-butene; from propene, yin,adm jr., 12/95
+CEL2 CEL1 CTL3 47.00 125.20 ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CEL1 52.00 119.50 ! 2-butene, yin,adm jr., 12/95
+HEL1 CEL1 CEL2 42.00 118.00 ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2 40.00 116.00 ! 1-butene; from propene, yin,adm jr., 12/95
+HEL1 CEL1 CTL3 22.00 117.00 ! propene, yin,adm jr., 12/95
+HEL2 CEL2 CEL1 45.00 120.50 ! propene, yin,adm jr., 12/95
+HEL2 CEL2 CEL2 55.50 120.50 ! ethene, yin,adm jr., 12/95
+HEL2 CEL2 HEL2 19.00 119.00 ! propene, yin,adm jr., 12/95
+CEL1 CTL2 CTL2 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95
+CEL1 CTL2 CTL3 32.00 112.20 ! 1-butene; from propene, yin,adm jr., 12/95
+HAL2 CTL2 CEL1 45.00 111.50 ! 1-butene; from propene, yin,adm jr., 12/95
+HAL3 CTL3 CEL1 42.00 111.50 ! 2-butene, yin,adm jr., 12/95
+CEL1 CTL2 CEL1 30.0 114.0 ! 1,4-dipentene, adm jr., 2/00
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types Kchi n delta
+!
+!Heme to Sulfate (PSUL) link
+X FE SS X 0.0000 4 0.00 ! guess
+ !adm jr., 7/01
+X CS SS X 0.0000 3 0.20 ! guess
+ !from methanethiol, HS S CT3 HA
+ !adm jr., 7/01
+
+C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89
+CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
+ ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c
+CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL
+ ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c
+CE1 CE1 CT3 HA 0.0300 3 0.00 !
+ ! for butene, yin/adm jr., 12/95
+CE2 CE1 CT2 CT3 0.5000 1 180.00 !
+ ! 1-butene, adm jr., 2/00 update
+CE2 CE1 CT2 CT3 1.3000 3 180.00 !
+ ! 1-butene, adm jr., 2/00 update
+CE2 CE1 CT2 HA 0.1200 3 0.00 !
+ ! for butene, yin/adm jr., 12/95
+CE2 CE1 CT3 HA 0.0500 3 180.00 !
+ ! for propene, yin/adm jr., 12/95
+CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
+ ! ethylbenzene ethyl rotation, adm jr. 3/7/92
+CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
+ ! from ethylbenzene, adm jr., 3/7/92
+CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
+ ! from ethylbenzene, adm jr., 3/7/92
+CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP
+ ! from CT2 C NH1 CT2, adm jr. 10/21/96
+CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
+ ! from CT2 C NH1 CT2, adm jr. 10/21/96
+CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 toluene and ethylbenzene
+CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
+CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2
+CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO
+ ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89
+CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92, butane trans/gauche
+CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP
+ ! from CT2 CT1 NH1 C, for lactams, adm jr.
+CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK
+CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
+ !JWK
+CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
+CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION
+ ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
+CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
+CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP
+ ! for acetylated GLY N-terminus, adm jr.
+CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
+ ! for acetylated GLY N-terminus, adm jr.
+CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! toluene, adm jr., 3/7/92
+CT3 CE1 CE2 HE2 5.2000 2 180.00 !
+ ! for propene, yin/adm jr., 12/95
+CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2
+CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI
+ ! ethylbenzene ethyl rotation, adm jr. 3/7/92
+CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
+ ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92
+CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92, butane trans/gauche
+CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92, butane trans/gauche
+CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO
+ ! from ethylbenzene, adm jr., 3/7/92
+CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO
+ ! from ethylbenzene, adm jr., 3/7/92
+CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION
+ ! expt. MeEtS, 3/26/92 (FL)
+CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION
+ ! DTN 8/24/90
+CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP
+ ! Revised to adjust NMA cis/trans energy difference. (LK)
+CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION
+ ! expt. MeEtS, 3/26/92 (FL)
+CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION
+ ! expt. MeEtS, 3/26/92 (FL)
+CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
+CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION
+ ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL)
+CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION
+ ! improved CSSC dihedral in DMDS 5/15/92 (FL)
+CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL
+ ! adm jr. 5/02/91, acetic acid pure solvent
+H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
+ ! from H NH1 CT2 CT3, for lactams, adm jr.
+H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
+ ! adm jr. 4/10/91, acetamide update
+H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
+ ! adm jr. 4/10/91, acetamide update
+H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
+ ! adm jr. 4/10/91, acetamide update
+H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 7/20/89
+H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
+H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H
+H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
+H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA
+H NY CA CY 0.8000 2 180.00 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC
+ ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92
+H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC
+ ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC
+ ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93
+HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO
+ ! adm jr., 10/02/89
+HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO
+ ! ADM JR., 10/02/89
+HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
+ ! TRP (JES)
+HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO
+ ! JWK
+HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
+ ! JWK
+HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HA CA NY H 1.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL
+ ! adm jr. 4/10/91, acetamide update
+HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
+ ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
+HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO
+ ! JWK
+HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO
+ ! JWK
+HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION
+ ! DTN 8/24/90
+HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO
+ ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89
+HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION
+ ! DTN 8/24/90
+HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+HE1 CE1 CE1 HE1 1.0000 2 180.00 !
+ ! 2-butene, adm jr., 8/98 update
+CT3 CE1 CE1 HE1 1.0000 2 180.00 !
+ ! 2-butene, adm jr., 8/98 update
+HE1 CE1 CE2 HE2 5.2000 2 180.00 !
+ ! for propene, yin/adm jr., 12/95
+HE1 CE1 CT2 HA 0.0000 3 0.00
+ ! butene, adm jr., 2/00 update
+HE1 CE1 CT2 CT3 0.1200 3 0.00 !
+ ! for butene, yin/adm jr., 12/95
+HE1 CE1 CT3 HA 0.0000 3 0.00
+ ! butene, adm jr., 2/00 update
+HE2 CE2 CE1 CT2 5.2000 2 180.00 !
+ ! for butene, yin/adm jr., 12/95
+HE2 CE2 CE1 CPB 5.2000 2 180.00 !
+ ! for vinyl, from butene, yin/adm jr., 12/95
+HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+HC NH2 CT2 CT2 0.1100 3 0.00
+ !from X CT3 NH2 X, neutral lysine
+HC NH2 CT2 HA 0.1100 3 0.00
+ !from X CT3 NH2 X, neutral lysine
+HC NH2 CT2 HB 0.1100 3 0.00
+ !from X CT3 NH2 X, neutral glycine, adm jr.
+HC NH2 CT2 CD 0.1100 3 0.00
+ !from X CT3 NH2 X, neutral glycine, adm jr.
+HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 benzene
+HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 toluene and ethylbenzene
+HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO
+ ! toluene, adm jr., 3/7/92
+HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 benzene
+HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK indole 05/14/91
+HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO
+ ! JWK indole 05/14/91
+HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO
+ !adm jr., 12/30/91, for jwk
+HP CA NY H 0.4000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90, his
+HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90, YES, 0.0
+HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION
+ ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
+HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION
+ ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
+HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION
+ ! ethanethiol C-C-S-H surface, adm jr., 4/18/93
+HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION
+ ! methanethiol pure solvent, adm jr., 6/22/92
+N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO
+ ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92
+NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK)
+NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP
+ ! from NH1 C CT1 CT2, for lactams, adm jr.
+NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP
+ ! LK for autogenerate dihe, sp2-methyl, no dihedral potential
+NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93
+NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! adm jr. 3/24/92, for PRES GLYP
+NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
+NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA
+NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
+NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA
+NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
+ ! HIS CB-CG TORSION,
+NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
+ ! HIS CB-CG TORSION,
+NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
+ ! HIS CB-CG TORSION,
+NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO
+ ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89
+NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO
+ ! his, ADM JR., 7/20/89
+NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO
+ ! JWK
+NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO
+ ! JWK indole 05/14/91
+NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO
+ ! JWK 09/05/89
+NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO
+ ! JWK 05/14/91 fit to indole
+O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP
+ ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c
+O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! Backbone parameter set made complete RLD 8/8/90
+O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP
+ ! from O C CT1 CT2, for lactams, adm jr.
+O C CT2 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP
+ ! Alanine Dipeptide ab initio calc's (LK)
+O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO
+ ! Backbone parameter set made complete RLD 8/8/90
+O C CT3 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O C N CP1 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C N CP1 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C N CP3 2.7500 2 180.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C N CP3 0.3000 4 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O C NH1 H 2.5000 2 180.00 ! ALLOW PEP
+ ! Gives appropriate NMA cis/trans barrier. (LK)
+O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL
+ ! adm jr. 4/05/91, for asn,asp,gln,glu and cters
+O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO
+ ! adm jr. 4/10/91, acetamide update
+OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! adm jr. 8/27/91, phenoxide
+OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO
+ ! adm jr. 8/27/91, phenoxide
+OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
+ ! adm jr. 4/17/94, zwitterionic glycine
+OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO
+ ! adm jr. 4/17/94, zwitterionic glycine
+OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 phenol
+OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO
+ ! JES 8/25/89 phenol
+S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
+ ! DTN 8/24/90
+SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION
+ ! DTN 8/24/90
+SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI
+ ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
+SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI
+ ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90
+SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
+SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION
+ ! expt. dimethyldisulfide, 3/26/92 (FL)
+SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL
+ ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92
+!X C C X 4.0000 2 180.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO
+ ! 9.0->2.25 GUANIDINIUM (KK)
+X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC
+ ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier
+X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CE1 CE1 X 0.1500 1 0.00
+ ! 2-butene, adm jr., 2/00 update
+X CE1 CE1 X 8.5000 2 180.00
+ ! 2-butene, adm jr., 2/00 update
+X CE2 CE2 X 4.9000 2 180.00 !
+ ! for ethene, yin/adm jr., 12/95
+X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! changed to 0.0 RLD 5/19/92
+X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92
+X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+X CPB CE1 X 3.0000 2 180.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO
+ ! JWK indole 05/14/91
+X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
+ ! 0.715->0.10 METHYLAMMONIUM (KK)
+X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
+ ! EMB 11/21/89 methanol vib fit
+X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
+ ! toluene, adm jr., 3/7/92
+X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI
+ ! rotation barrier in Ethane (SF)
+X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
+ ! methylguanidinium, adm jr., 3/26/92
+X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL
+ ! 0.715->0.10 METHYLAMMONIUM (KK)
+X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
+ ! EMB 11/21/89 methanol vib fit
+X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO
+ ! toluene, adm jr., 3/7/92
+X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP
+ ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK)
+X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL
+ ! methylguanidinium, adm jr., 3/26/92
+X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL
+ ! methylamine geom/freq, adm jr., 6/2/92
+X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL
+ ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92
+X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO
+ ! EMB 11/21/89 methanol vib fit
+X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL
+ ! adm jr. 3/19/92, from lipid methyl acetate
+X FE CM X 0.0500 4 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): ligands (KK 05/13/91)
+X FE NPH X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): for "ic para" only (KK 05/13/91)
+X FE OM X 0.0000 4 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): ligands (KK 05/13/91)
+X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM
+ ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91)
+!lipid section
+X CTL1 OHL X 0.14 3 0.00 ! glycerol
+X CTL2 OHL X 0.14 3 0.00 ! glycerol
+X CTL3 OHL X 0.14 3 0.00 ! glycerol
+OBL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid
+OBL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid
+OSL CL CTL2 HAL2 0.00 6 180.00 ! acetic acid
+OSL CL CTL3 HAL3 0.00 6 180.00 ! acetic acid
+OBL CL OSL CTL1 0.965 1 180.00 ! methyl acetate
+OBL CL OSL CTL1 3.85 2 180.00 ! methyl acetate
+OBL CL OSL CTL2 0.965 1 180.00 ! methyl acetate
+OBL CL OSL CTL2 3.85 2 180.00 ! methyl acetate
+OBL CL OSL CTL3 0.965 1 180.00 ! methyl acetate
+OBL CL OSL CTL3 3.85 2 180.00 ! methyl acetate
+X CL OSL X 2.05 2 180.00 ! methyl acetate
+X CTL2 CL X 0.05 6 180.00 ! methyl acetate
+X CTL3 CL X 0.05 6 180.00 ! methyl acetate
+X CL OHL X 2.05 2 180.00 ! acetic acid
+HAL2 CTL2 CL OHL 0.00 6 180.00
+HAL3 CTL3 CL OHL 0.00 6 180.00
+OSL PL OSL CTL2 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr.
+OSL PL OSL CTL2 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr.
+OSL PL OSL CTL2 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr.
+O2L PL OSL CTL2 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
+OSL PL OSL CTL3 1.20 1 180.00 ! phosphate, new NA, 4/98, adm jr.
+OSL PL OSL CTL3 0.10 2 180.00 ! phosphate, new NA, 4/98, adm jr.
+OSL PL OSL CTL3 0.10 3 180.00 ! phosphate, new NA, 4/98, adm jr.
+O2L PL OSL CTL3 0.10 3 0.00 ! phosphate, new NA, 4/98, adm jr.
+OHL PL OSL CTL2 0.95 2 0.00 ! terminal phosphate
+OHL PL OSL CTL2 0.50 3 0.00 ! terminal phosphate
+OHL PL OSL CTL3 0.95 2 0.00 ! terminal phosphate
+OHL PL OSL CTL3 0.50 3 0.00 ! terminal phosphate
+X OHL PL X 0.30 3 0.00 ! terminal phosphate
+X CTL1 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
+X CTL2 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
+X CTL3 OSL X 0.00 3 0.00 ! phosphate, new NA, 4/98, adm jr.
+CTL3 CTL2 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92
+CTL2 CTL2 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92
+CTL3 CTL1 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92
+CTL2 CTL1 OSL CL 0.7 1 180.00 ! ethyl acetate, 12/92
+CTL1 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92
+CTL1 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92
+CTL2 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92
+CTL2 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92
+CTL3 CTL2 CL OSL -0.15 1 180.00 ! methyl propionate, 12/92
+CTL3 CTL2 CL OSL 0.53 2 180.00 ! methyl propionate, 12/92
+X CTL2 NTL X 0.26 3 0.00 ! tetramethylammonium
+X CTL5 NTL X 0.23 3 0.00 ! tetramethylammonium
+X CTL2 NH3L X 0.10 3 0.00 ! ethanolamine
+NH3L CTL2 CTL2 OHL 0.7 1 180.00 ! ethanolamine
+NH3L CTL2 CTL2 OSL 0.7 1 180.00 ! ethanolamine
+NTL CTL2 CTL2 OHL 4.3 1 180.00 ! choline, 12/92
+NTL CTL2 CTL2 OHL -0.4 3 180.00 ! choline, 12/92
+NTL CTL2 CTL2 OSL 3.3 1 180.00 ! choline, 12/92
+NTL CTL2 CTL2 OSL -0.4 3 180.00 ! choline, 12/92
+X CTL1 CTL1 X 0.200 3 0.00 ! alkane, 3/92
+X CTL1 CTL2 X 0.200 3 0.00 ! alkane, 3/92
+X CTL1 CTL3 X 0.200 3 0.00 ! alkane, 3/92
+X CTL2 CTL2 X 0.1900 3 0.00 ! alkane, 4/98, yin and mackerell
+X CTL2 CTL3 X 0.1600 3 0.00 ! alkane, 4/98, yin and mackerell
+X CTL3 CTL3 X 0.1525 3 0.00 ! alkane, 4/98, yin and mackerell
+CTL3 CTL2 CTL2 CTL3 0.10 2 180.00 ! alkane, 4/98, adm jr., lower butane gauche conformer
+CTL3 CTL2 CTL2 CTL3 0.15 4 0.00 ! alkane, 4/98, adm jr.
+CTL3 CTL2 CTL2 CTL3 0.10 6 180.00 ! alkane, 4/98, adm jr.
+CTL2 CTL2 CTL2 CTL3 0.10 2 180.00 ! alkane, 4/98, adm jr.
+CTL2 CTL2 CTL2 CTL3 0.15 4 0.00 ! alkane, 4/98, adm jr.
+CTL2 CTL2 CTL2 CTL3 0.10 6 180.00 ! alkane, 4/98, adm jr.
+CTL2 CTL2 CTL2 CTL2 0.10 2 180.00 ! alkane, 4/98, adm jr.
+CTL2 CTL2 CTL2 CTL2 0.15 4 0.00 ! alkane, 4/98, adm jr.
+CTL2 CTL2 CTL2 CTL2 0.10 6 180.00 ! alkane, 4/98, adm jr.
+HAL3 CTL3 OSL SL 0.00 3 0.00 ! methylsulfate
+CTL2 OSL SL O2L 0.00 3 0.00 ! methylsulfate
+CTL3 OSL SL O2L 0.00 3 0.00 ! methylsulfate
+HEL1 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update
+CTL3 CEL1 CEL1 HEL1 1.0000 2 180.00 ! 2-butene, adm jr., 8/98 update
+X CEL1 CEL1 X 0.1500 1 0.00 ! 2-butene, adm jr., 2/00 update
+X CEL1 CEL1 X 8.5000 2 180.00 ! 2-butene, adm jr., 2/00 update
+X CEL2 CEL2 X 4.9000 2 180.00 ! ethene, yin,adm jr., 12/95
+CTL2 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95
+CTL3 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CEL2 HEL2 5.2000 2 180.00 ! propene, yin,adm jr., 12/95
+CEL1 CEL1 CTL2 HAL2 0.0300 3 0.00 ! butene, yin,adm jr., 12/95
+CEL1 CEL1 CTL3 HAL3 0.0300 3 0.00 ! butene, yin,adm jr., 12/95
+CEL1 CEL1 CTL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update
+CEL1 CEL1 CTL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update
+CEL1 CEL1 CTL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update
+CEL1 CEL1 CTL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 CTL2 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 CTL2 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 CTL3 0.5000 1 180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 CTL3 1.3000 3 180.00 ! 1-butene, adm jr., 2/00 update
+CEL2 CEL1 CTL2 HAL2 0.1200 3 0.00 ! 1-butene, yin,adm jr., 12/95
+CEL2 CEL1 CTL3 HAL3 0.0500 3 180.00 ! propene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! butene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2 CTL3 0.1200 3 0.00 ! butene, yin,adm jr., 12/95
+HEL1 CEL1 CTL2 HAL2 0.0000 3 0.00 ! butene, adm jr., 2/00 update
+HEL1 CEL1 CTL3 HAL3 0.0000 3 0.00 ! butene, adm jr., 2/00 update
+! 1,4-dipentene, adm jr., 2/00
+CEL2 CEL1 CTL2 CEL1 1.200 1 180.00 !1,4-dipentene
+CEL2 CEL1 CTL2 CEL1 0.400 2 180.00 !1,4-dipentene
+CEL2 CEL1 CTL2 CEL1 1.300 3 180.00 !1,4-dipentene
+CEL1 CTL2 CEL1 HEL1 0.000 2 0.00 !1,4-dipentene
+CEL1 CTL2 CEL1 HEL1 0.000 3 0.00 !1,4-dipentene
+! 2,5-diheptene, adm jr., 2/00
+! for CIS double bonds in polyunsaturated lipids (default)
+CEL1 CEL1 CTL2 CEL1 1.000 1 180.00 !2,5-diheptane
+CEL1 CEL1 CTL2 CEL1 0.100 2 0.00 !2,5-diheptane
+CEL1 CEL1 CTL2 CEL1 0.300 3 180.00 !2,5-diheptane
+CEL1 CEL1 CTL2 CEL1 0.200 4 0.00 !2,5-diheptane
+! for TRANS double bonds in polyunsaturated lipids
+! uncomment following 4 lines and comment previous 4 lines to use
+!CEL1 CEL1 CTL2 CEL1 1.200 1 180.00 !2,5-diheptane
+!CEL1 CEL1 CTL2 CEL1 0.200 2 180.00 !2,5-diheptane
+!CEL1 CEL1 CTL2 CEL1 1.200 3 180.00 !2,5-diheptane
+!CEL1 CEL1 CTL2 CEL1 0.100 4 180.00 !2,5-diheptane
+! methylbutyrate
+CTL3 CTL2 CTL2 CL 0.21 1 180.00 !
+CTL3 CTL2 CTL2 CL 0.39 2 0.00 !
+CTL3 CTL2 CTL2 CL 0.35 3 180.00 !
+CTL3 CTL2 CTL2 CL 0.11 4 0.00 !
+CTL3 CTL2 CTL2 CL 0.09 6 180.00 !
+CTL2 CTL2 CTL2 CL 0.21 1 180.00 !
+CTL2 CTL2 CTL2 CL 0.39 2 0.00 !
+CTL2 CTL2 CTL2 CL 0.35 3 180.00 !
+CTL2 CTL2 CTL2 CL 0.11 4 0.00 !
+CTL2 CTL2 CTL2 CL 0.09 6 180.00 !
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types Kpsi psi0
+!
+CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPB X X CE1 90.0000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+!HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! Heme vinyl substituent (KK, from propene (JCS))
+HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+!HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO
+ ! Heme (6-liganded): substituents (KK 05/13/91)
+!HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO
+ ! Heme vinyl substituent (KK, from propene (JCS))
+HE2 HE2 CE2 CE2 3.0 0 0.00 !
+ ! for ethene, yin/adm jr., 12/95
+HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! 5.75->40.0 GUANIDINIUM (KK)
+NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! NMA Vibrational Modes (LK)
+NH2 X X H 4.0000 0 0.0000 ! ALLOW POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 7/05/90
+NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO
+ ! his, adm jr., 6/27/90
+NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO
+ !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf.
+O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! adm jr., 5/13/91, formamide geometry and vibrations
+O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO
+ ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92
+O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 8/13/90 acetamide geometry and vibrations
+O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL
+ ! adm jr., 5/13/91, formamide geometry and vibrations
+O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO
+ ! NMA Vibrational Modes (LK)
+OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL
+ ! adm jr., 10/17/90, acetic acid vibrations
+OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+CC X X CT1 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+CC X X CT2 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+CC X X CT3 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION
+ ! 90.0->96.0 acetate, single impr (KK)
+!lipid section
+OBL X X CL 100.00 0 0.00 ! acetic acid
+HEL2 HEL2 CEL2 CEL2 3.00 0 0.00 ! ethene, yin,adm jr., 12/95
+OCL X X CL 96.00 0 0.00 ! acetate
+
+CMAP
+! 2D grid correction data. The following surfaces are the correction
+! to the CHARMM22 phi, psi alanine, proline and glycine dipeptide surfaces.
+! Use of CMAP requires generation with the topology file containing the
+! CMAP specifications along with version 31 or later of CHARMM. Note that
+! use of "skip CMAP" yields the charmm22 energy surfaces.
+!
+! references
+!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Accurate Treatment of
+!Protein Backbone Conformational Energetics in Empirical Force Fields, Submitted
+!for publication.
+
+!MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of the
+!Protein Backbone in Empirical Force Fields, Journal of the American Chemical
+!Society, In Press.
+
+
+! alanine map
+C NH1 CT1 C NH1 CT1 C NH1 24
+
+!-180
+0.126790 0.768700 0.971260 1.250970 2.121010
+2.695430 2.064440 1.764790 0.755870 -0.713470
+0.976130 -2.475520 -5.455650 -5.096450 -5.305850
+-3.975630 -3.088580 -2.784200 -2.677120 -2.646060
+-2.335350 -2.010440 -1.608040 -0.482250
+
+!-165
+-0.802290 1.377090 1.577020 1.872290 2.398990
+2.461630 2.333840 1.904070 1.061460 0.518400
+-0.116320 -3.575440 -5.284480 -5.160310 -4.196010
+-3.276210 -2.715340 -1.806200 -1.101780 -1.210320
+-1.008810 -0.637100 -1.603360 -1.776870
+
+!-150
+-0.634810 1.156210 1.624350 2.047200 2.653910
+2.691410 2.296420 1.960450 1.324930 2.038290
+-1.151510 -3.148610 -4.058280 -4.531850 -3.796370
+-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
+-1.039340 -1.618060 -1.725460 -1.376360
+
+!-135
+0.214000 1.521370 1.977440 2.377950 2.929470
+2.893410 2.435810 2.162970 1.761500 1.190090
+-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
+-1.836030 -0.957950 0.021790 -0.032760 -0.665880
+-1.321170 -1.212320 -0.893170 -0.897040
+
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+! glycine before proline map: use glycine map
+
+C NH1 CT2 C NH1 CT2 C N 24
+
+!-180
+-0.549160 -0.535500 -0.588110 -0.754620 -0.679290
+-0.038150 0.298460 0.326040 -0.375610 -1.704360
+-3.061280 -3.956460 -3.576280 -1.038930 2.012450
+-1.714610 -0.377660 0.317310 0.294580 -0.042920
+-0.676620 -0.744600 -0.586590 -0.554770
+
+!-165
+-0.709450 -0.896700 -0.990850 -1.319240 -0.940260
+-0.126160 0.329180 0.258100 -0.534910 -1.715700
+-2.780320 -3.153350 -1.636020 1.822690 -2.675640
+-1.810120 -0.410680 0.180860 0.196710 -0.000430
+-0.271890 -0.462500 -0.348750 -0.477660
+
+!-150
+-1.224850 -1.482430 -1.665900 -1.656770 -1.119780
+-1.642540 -0.054220 -0.290670 -0.887080 -1.626260
+-2.165440 -1.546500 0.753400 -2.949180 -2.225630
+-1.664160 -0.628990 0.000490 0.033160 -0.092820
+-0.339050 -0.563330 -0.794980 -0.710760
+
+!-135
+-1.787640 -2.117750 -2.143020 -1.803720 -1.567160
+-0.886880 -0.801350 -0.851590 -1.020630 -1.337360
+-1.062570 0.338010 -4.372310 -2.435890 -2.220710
+-1.718060 -0.758950 -0.207560 0.100910 -0.055650
+-0.288370 -0.880610 -1.267450 -1.465530
+
+!-120
+-2.348270 -2.593790 -2.596140 -2.364070 -1.970070
+-1.705860 -1.435540 -1.289220 -1.358170 -0.975570
+-3.514390 -4.283210 -3.975820 -3.215190 -2.394430
+-1.455320 -0.553910 -0.158900 -0.173830 -0.297950
+-0.661220 -1.068330 -1.601800 -1.914850
+
+!-105
+-2.788800 -3.079570 -3.178150 -3.013710 -2.626630
+-2.266680 -1.951490 -1.681850 -1.195390 -2.567680
+-3.632800 -4.748210 -4.662850 -4.255190 -2.776760
+-1.695490 -0.893140 -0.633810 -0.467320 -0.540540
+-0.950190 -1.401500 -1.959970 -2.412680
+
+!-90
+-3.857170 -3.713610 -3.902110 -3.611370 -3.040850
+-2.406460 -1.975250 -1.452040 -0.971860 -2.808170
+-4.181160 -4.981430 -5.446890 -4.359900 -2.864390
+-1.898510 -1.139090 -0.971340 -1.065550 -1.020680
+-1.141350 -1.794480 -2.420970 -2.939990
+
+!-75
+-4.987770 -4.995210 -4.485310 -3.892550 -3.228630
+-2.345360 -1.664160 -1.105500 -1.945510 -3.715530
+-4.492140 -5.536170 -5.708500 -3.675410 -2.986660
+-1.859410 -0.756620 -1.269930 -1.312730 -1.607440
+-1.892510 -2.659400 -3.347950 -3.970600
+
+!-60
+-6.183650 -5.456080 -4.878940 -4.000820 -2.683230
+-2.067520 -1.094850 -1.119790 -2.962910 -3.687830
+-4.993340 -4.666260 -3.796280 -3.374140 -2.495430
+-1.453990 -0.877560 -1.002930 -1.337310 -2.431360
+-2.948140 -4.008100 -4.821040 -5.565810
+
+!-45
+-6.755760 -5.850030 -4.362190 -2.714090 -1.708710
+-0.526660 -0.536700 -2.037170 -3.892650 -4.558570
+-4.237410 -3.735160 -3.688580 -3.009910 -2.112940
+-1.455400 -0.925490 -1.121840 -1.561900 -2.751370
+-4.094860 -5.207530 -6.128530 -6.613030
+
+!-30
+-5.716250 -4.434060 -2.788600 -0.974400 -0.729200
+-0.904940 -1.833540 -3.017700 -3.313450 -3.336010
+-3.181640 -3.594720 -1.231370 -0.603790 0.128810
+-1.222610 -0.909150 -0.837700 -1.346820 -3.040880
+-4.731110 -5.844860 -6.428460 -6.424880
+
+!-15
+-3.991110 -2.046000 0.082550 -2.676110 -2.828500
+-2.596640 -2.843330 -3.011480 -2.312640 -2.405980
+-3.086210 -1.164620 -1.231660 -0.871900 -0.348980
+-1.735900 -0.914150 -0.484520 -1.818040 -3.602550
+-5.330320 -5.992270 -5.588080 -5.408360
+
+!0
+-1.147060 -3.317730 -4.305100 -4.615200 -4.533780
+-3.622950 -2.832800 -1.872810 -1.144300 -1.994070
+-0.741980 -1.115010 -1.229250 -1.103680 -0.742430
+-1.973970 -1.070020 -1.802220 -2.712770 -3.624130
+-4.537100 -4.619970 -4.310890 -3.318290
+
+!15
+-3.997710 -5.408360 -5.588080 -5.992270 -5.330320
+-3.602550 -1.818040 -0.484520 -0.914150 -1.735900
+-0.348980 -0.871900 -1.231660 -1.164620 -3.086210
+-2.405980 -2.312640 -3.011480 -2.843330 -2.596640
+-2.828500 -2.676110 0.082550 -2.046000
+
+!30
+-5.710850 -6.424880 -6.428460 -5.844860 -4.731110
+-3.040880 -1.346820 -0.837700 -0.909150 -1.222610
+0.128810 -0.603790 -1.231370 -3.594720 -3.181640
+-3.336010 -3.313450 -3.017700 -1.833540 -0.904940
+-0.729200 -0.974400 -2.788600 -4.434060
+
+!45
+-6.754940 -6.613030 -6.128530 -5.207530 -4.094860
+-2.751370 -1.561900 -1.121840 -0.925490 -1.455400
+-2.112940 -3.009910 -3.688580 -3.735160 -4.237410
+-4.558570 -3.892650 -2.037170 -0.536700 -0.526660
+-1.708710 -2.714090 -4.362190 -5.850030
+
+!60
+-6.188070 -5.565810 -4.821040 -4.008100 -2.948140
+-2.431360 -1.337310 -1.002930 -0.877560 -1.453990
+-2.495430 -3.374140 -3.796280 -4.666260 -4.993340
+-3.687830 -2.962910 -1.119790 -1.094850 -2.067520
+-2.683230 -4.000820 -4.878940 -5.456080
+
+!75
+-4.986080 -3.970600 -3.347950 -2.659400 -1.892510
+-1.607440 -1.312730 -1.269930 -0.756620 -1.859410
+-2.986660 -3.675410 -5.708500 -5.536170 -4.492140
+-3.715530 -1.945510 -1.105500 -1.664160 -2.345360
+-3.228630 -3.892550 -4.485310 -4.995210
+
+!90
+-3.879190 -2.939990 -2.420970 -1.794480 -1.141350
+-1.020680 -1.065550 -0.971340 -1.139090 -1.898510
+-2.864390 -4.359900 -5.446890 -4.981430 -4.181160
+-2.808170 -0.971860 -1.452040 -1.975250 -2.406460
+-3.040850 -3.611370 -3.902110 -3.713610
+
+!105
+-2.793280 -2.412680 -1.959970 -1.401500 -0.950190
+-0.540540 -0.467320 -0.633810 -0.893140 -1.695490
+-2.776760 -4.255190 -4.662850 -4.448210 -3.332800
+-2.567680 -1.195390 -1.681850 -1.951490 -2.266680
+-2.626630 -3.013710 -3.178150 -3.079570
+
+!120
+-2.330190 -1.914850 -1.601800 -1.068330 -0.661220
+-0.297950 -0.173830 -0.158900 -0.553910 -1.455320
+-2.394430 -3.215190 -3.975820 -3.783210 -3.014390
+-0.975570 -1.358170 -1.289220 -1.435540 -1.705860
+-1.970070 -2.364070 -2.596140 -2.593790
+
+!135
+-1.796120 -1.465530 -1.267450 -0.880610 -0.288370
+-0.055650 0.100910 -0.207560 -0.758950 -1.718060
+-2.220710 -2.435890 -4.372310 0.338010 -1.062570
+-1.337360 -1.020630 -0.851590 -0.801350 -0.886880
+-1.567160 -1.803720 -2.143020 -2.117750
+
+!150
+-1.263610 -0.710760 -0.794980 -0.563330 -0.339050
+-0.092820 0.033160 0.000490 -0.628990 -1.664160
+-2.225630 -2.949180 0.753400 -1.546500 -2.165440
+-1.626260 -0.887080 -0.290670 -0.054220 -1.642540
+-1.119780 -1.656770 -1.665900 -1.482430
+
+!165
+-0.684660 -0.477660 -0.348750 -0.462500 -0.271890
+-0.000430 0.196710 0.180860 -0.410680 -1.810120
+-2.675640 1.822690 -1.636020 -3.153350 -2.780320
+-1.715700 -0.534910 0.258100 0.329180 -0.126160
+-0.940260 -1.319240 -0.990850 -0.896700
+
+NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
+cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
+ !adm jr., 5/08/91, suggested cutoff scheme
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
+!
+!carbons
+C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
+ ! NMA pure solvent, adm jr., 3/3/93
+CA 0.000000 -0.070000 1.992400 ! ALLOW ARO
+ ! benzene (JES)
+CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO
+ ! adm jr. 3/3/92, acetic acid heat of solvation
+CD 0.000000 -0.070000 2.000000 ! ALLOW POL
+ ! adm jr. 3/19/92, acetate a.i. and dH of solvation
+CE1 0.000000 -0.068000 2.090000 !
+ ! for propene, yin/adm jr., 12/95
+CE2 0.000000 -0.064000 2.080000 !
+ ! for ethene, yin/adm jr., 12/95
+CM 0.000000 -0.110000 2.100000 ! ALLOW HEM
+ ! Heme (6-liganded): CO ligand carbon (KK 05/13/91)
+CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! alkane update, adm jr., 3/2/92
+CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO
+ ! adm jr., 10/23/91, imidazole solvation and sublimation
+CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO
+ ! adm jr., 10/23/91, imidazole solvation and sublimation
+CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO
+ ! benzene (JES)
+CS 0.000000 -0.110000 2.200000 ! ALLOW SUL
+ ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
+CST 0.000000 -0.058000 1.563000 !
+ ! carbon dioxide, JES
+CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! isobutane pure solvent properties, adm jr, 2/3/92
+CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! propane pure solvent properties, adm jr, 2/3/92
+CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+CY 0.000000 -0.070000 1.992400 ! ALLOW ARO
+ ! TRP, JWK 08/29/89
+!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
+CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! from CT1x: needs work
+CT1x 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92: needs work
+CT2x 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+CT3x 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+! hydrogens
+H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC
+ ! same as TIP3P hydrogen, adm jr., 7/20/89
+HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+HE1 0.000000 -0.031000 1.250000 !
+ ! for propene, yin/adm jr., 12/95
+HE2 0.000000 -0.026000 1.260000 !
+ ! for ethene, yin/adm jr., 12/95
+HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC
+ ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92
+HC 0.000000 -0.046000 0.224500 ! ALLOW POL
+ ! new, small polar Hydrogen, see also adm jr. JG 8/27/89
+HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO
+ ! JES 8/25/89 values from Jorgensen fit to hydration energy
+HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO
+ ! adm jr., 6/27/90, his
+HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO
+ ! adm jr., 6/27/90, his
+HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO
+ ! adm jr., 3/24/92, maintain old aliphatic H VDW params
+HS 0.000000 -0.100000 0.450000 ! ALLOW SUL
+ ! methanethiol pure solvent, adm jr., 6/22/92
+HT 0.000000 -0.046000 0.224500 ! ALLOW WAT
+ !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete
+!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str)
+HA1 0.0 -0.022 1.3200 ! alkane, 3/92
+HA2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98
+HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98
+!nitrogens
+N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO
+ ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93
+NC2 0.000000 -0.200000 1.850000 ! ALLOW POL
+ ! JG 8/27/89; note: NH1 in ARG was changed to NC2.
+NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO
+ ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
+NH2 0.000000 -0.200000 1.850000 ! ALLOW POL
+ ! adm jr.
+NH3 0.000000 -0.200000 1.850000 ! ALLOW POL
+ ! adm jr.
+NP 0.000000 -0.200000 1.850000 ! ALLOW PRO
+ ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90
+NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM
+ ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91)
+NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! His, adm jr., 9/4/89
+NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! His, adm jr., 9/4/89
+NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! His, adm jr., 9/4/89
+NY 0.000000 -0.200000 1.850000 ! ALLOW ARO
+ ! trp, JWK
+! oxygens
+O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL
+ ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)
+OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO
+ ! adm jr., 10/17/90, acetic acid carbonyl O
+OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION
+ ! JG 8/27/89
+OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
+ ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)
+OM 0.000000 -0.120000 1.700000 ! ALLOW HEM
+ ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91)
+OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO
+ ! adm jr. 9/17/90, avoid O* wildcard
+OST 0.000000 -0.165000 1.692000 !
+ ! carbon dioxide, JES
+OT 0.000000 -0.152100 1.768200 ! ALLOW WAT
+ !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete
+! sulfurs
+S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION
+ ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent
+SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION
+ ! adm jr., 3/3/92, dimethyldisulphide pure solvent
+SS 0.000000 -0.470000 2.200000 ! ALLOW SUL
+ ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92
+! ions and miscellaneous types
+SOD 0.0 -0.0469 1.36375 ! sodium
+ ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol
+POT 0.0 -0.0870 1.76375 ! potassium
+ ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
+CLA 0.0 -0.150 2.27 ! chloride
+ ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
+CAL 0.0 -0.120 1.367 ! Calcium
+ ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
+!CAL 0.000000 -0.120000 1.710000 ! Calcium (BP) in proteins prior
+ ! to 2003; not recommended due to need for NBFIX terms
+MG 0.0 -0.0150 1.18500 ! Magnesium
+ ! B. Roux dA = -441.65
+CES 0.0 -0.1900 2.100
+ ! Cesium, so far untested.
+ZN 0.000000 -0.250000 1.090000 ! ALLOW ION
+ ! RHS March 18, 1990
+FE 0.010000 0.000000 0.650000 ! ALLOW HEM
+ ! Heme (6-liganded): Iron atom (KK 05/13/91)
+HE 0.000000 -0.021270 1.4800 !
+ ! helium, experimental pot. energy surface, adm jr., 12/95
+NE 0.000000 -0.086000 1.5300
+ ! neon, semiempirical pot. energy surface, adm jr., 12/95
+CLAL 0.000000 -0.030000 1.908200 ! chlorine from Jorgensen/BOSS
+ ! for choroacetaldehyde
+DUM 0.000000 -0.000000 0.000000 !
+ ! dummy atom
+!pyridine series LJ parametes (see toppar_pyridines.str)
+CAP 0.000000 -0.070000 1.992400 !
+FA 0.000000 -0.12000 1.700000
+ ! from 1,3-difluorobenzene pure solvent
+CN 0.000000 -0.200000 1.750000 ! cyanopyridine
+NC 0.000000 -0.600000 1.850000 ! cyanopyridine
+OCA 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! 3acp
+COA 0.000000 -0.110000 2.000000 ! 3acp
+!fluorinated alkanes LJ parameters (see toppar_fluoro_alkanes.str)
+CF1 0.000000 -0.060000 1.900000
+CF2 0.000000 -0.042000 2.050000
+CF3 0.000000 -0.020000 2.300000
+HF1 0.000000 -0.028000 1.3200
+HF2 0.000000 -0.030000 1.3000
+F1 0.0 -0.135 1.63
+F2 0.0 -0.105 1.63
+F3 0.0 -0.097 1.60
+!protein model compounds (see toppar_all22_prot_model.str)
+C3 0.000000 -0.020000 2.275000 ! cyclopropane, JMW and CBP 4/04
+!retinol model compounds
+CC1A 0.0 -0.0680 2.0900 !
+CC1B 0.0 -0.0680 2.0900 !
+CC2 0.0 -0.0640 2.0800 !
+NS1 0.000000 -0.200000 1.850000 !N for deprotonated Schiff's base
+NS2 0.000000 -0.200000 1.850000 !N for protonated Schiff's base
+!lipid section
+HOL 0.0 -0.046 0.2245
+HAL1 0.0 -0.022 1.3200 ! alkane, 3/92
+HAL2 0.0 -0.028 1.3400 ! alkane, yin and mackerell, 4/98
+HAL3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98
+HCL 0.0 -0.046 0.2245 ! ethanolamine
+!HT 0.0 -0.046 0.2245
+HL 0.0 -0.046 0.7 ! polar H on NC4+
+HEL1 0.0 -0.031 1.25 ! alkene, yin,adm jr., 12/95
+HEL2 0.0 -0.026 1.26 ! alkene, yin,adm jr., 12/95
+!
+CL 0.0 -0.070 2.00 ! methyl acetate update
+CTL1 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! alkane, 3/92
+CTL2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+CTL3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr.
+CTL5 0.0 -0.0800 2.06 0.0 -0.01 1.9 ! old CTL3
+ ! maintained for tetramethylammonium
+CEL1 0.0 -0.068 2.09 ! alkene, yin,adm jr., 12/95
+CEL2 0.0 -0.064 2.08 ! alkene, yin,adm jr., 12/95
+!
+OBL 0.0 -0.12 1.70 0.0 -0.12 1.4
+OCL 0.0 -0.12 1.70
+O2L 0.0 -0.12 1.70
+OHL 0.0 -0.1521 1.77
+OSL 0.0 -0.1521 1.77
+!OT 0.0 -0.1521 1.7682
+!
+NH3L 0.0 -0.20 1.85 ! ethanolamine
+NTL 0.0 -0.20 1.85 ! as all other nitogens
+!
+SL 0.0 -0.47 2.1 ! methylsulfate
+PL 0.0 -0.585 2.15 ! ADM Jr.
+!DUM 0.0 -0.00 0.0 ! dummy atom
+!
+! ions, note lack of NBFIXes
+!
+!SOD 0.0 -0.0469 1.36375 ! sodium
+ ! D. Beglovd and B. Roux, dA=-100.8 kcal/mol
+!POT 0.0 -0.0870 1.76375 ! potassium
+ ! D. Beglovd and B. Roux, dA=-82.36+2.8 = -79.56 kca/mol
+!CLA 0.0 -0.150 2.27 ! chloride
+ ! D. Beglovd and B. Roux, dA=-83.87+4.46 = -79.40 kcal/mol
+!CAL 0.0 -0.120 1.367 ! Calcium
+ ! S. Marchand and B. Roux, dA = -384.8 kcal/mol
+!MG 0.0 -0.0150 1.18500 ! Magnesium
+ ! B. Roux dA = -441.65
+!CES 0.0 -0.1900 2.100
+ ! Cesium, so far untested.
+!ZN 0.0 -0.250000 1.090000 !
+ ! RHS March 18, 1990
+
+
+HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
+ ! READ PARAM APPEND CARD
+ ! to append hbond parameters from the file: par_hbond.inp
+
+END
diff --git a/test/namd/plumed.dat b/test/namd/plumed.dat
new file mode 100644
index 000000000..d21247cc8
--- /dev/null
+++ b/test/namd/plumed.dat
@@ -0,0 +1,31 @@
+DISTANCE ATOMS=0,21 LABEL=C1 COMPONENTS
+VOLUME LABEL=vol
+ENERGY LABEL=ene
+
+COMBINE LABEL=x ARG=C1.x,C1.y,C1.z POWERS=2,2,2
+COMBINE LABEL=xx ARG=x POWERS=0.5
+
+#RESTRAINT ARG=C1 AT=1.1 KAPPA=10000.0
+
+#MOVINGRESTRAINT ARG=ene AT0=-8525.08 KAPPA0=0.024 AT1=-8000 STEP0=0 STEP1=10000
+#RESTRAINT ARG=ene AT=-8525.08 KAPPA=-0.0002 STRIDE=2
+
+RESTRAINT ARG=C1 AT=0.4 KAPPA=1000.0
+
+#RESTRAINT ARG=vol AT=6.8 KAPPA=100.0
+
+FLUSH STRIDE=100
+
+PRINT ARG=C1,vol,ene,C1.x,C1.y,C1.z STRIDE=1 FILE=COLVAR
+
+##PRINT ...
+## ARG=*.*
+## STRIDE=10
+## FILE=COLVAR_ALL
+##... PRINT
+
+DEBUG logActivity
+
+ENDPLUMED
+
+
diff --git a/test/simplemd/.gitignore b/test/simplemd/.gitignore
new file mode 100644
index 000000000..2ae9f99c3
--- /dev/null
+++ b/test/simplemd/.gitignore
@@ -0,0 +1,8 @@
+simplemd
+simplemd-static
+simplemd-dummy
+*.mod
+energies.dat
+output.xyz
+trajectory.xyz
+COLVAR
diff --git a/test/simplemd/Makefile b/test/simplemd/Makefile
new file mode 100644
index 000000000..a6823209c
--- /dev/null
+++ b/test/simplemd/Makefile
@@ -0,0 +1,37 @@
+
+-include ../../Makefile.conf
+-include ../../src/Plumed.inc
+
+SRC=routines.f90 simplemd.f90 ran1.f gasdev.f
+OBJ=routines.o simplemd.o ran1.o gasdev.o
+
+EXE=simplemd-dummy simplemd-static simplemd
+
+all: $(EXE)
+
+simplemd-dummy: $(OBJ) $(PLUMED_WRAPPER)
+ $(LDF90) $(PLUMED_LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+simplemd-static: $(OBJ) $(PLUMED_OBJ)
+ $(LDF90) $(PLUMED_LDFLAGS) $^ -o $@ $(PLUMED_LIBS) $(PLUMED_DYNAMIC_LIBS)
+
+simplemd: $(OBJ) $(PLUMED_SHARED_OBJ)
+ $(LDF90) $(PLUMED_LDFLAGS) $^ -o $@ $(PLUMED_LIBS)
+
+clean:
+ rm -f *.o
+ rm -f $(EXE)
+ rm -f *.mod
+ rm -f energies.dat output.xyz trajectory.xyz
+
+# this is due to module inclusion:
+simplemd.o: routines.o
+
+%.o : %.f90
+ $(FC) -c $(FFLAGS) $(DOUBLEPRECISION) $< -o $@
+
+%.o : %.f
+ $(FC) -c $(FFLAGS) $(DOUBLEPRECISION) $< -o $@
+
+
+
diff --git a/test/simplemd/gasdev.f b/test/simplemd/gasdev.f
new file mode 100644
index 000000000..6e9533f9a
--- /dev/null
+++ b/test/simplemd/gasdev.f
@@ -0,0 +1,23 @@
+ FUNCTION gasdev(idum)
+ INTEGER idum
+ REAL gasdev
+CU USES ran1
+ INTEGER iset
+ REAL fac,gset,rsq,v1,v2,ran1
+ SAVE iset,gset
+ DATA iset/0/
+ if (iset.eq.0) then
+1 v1=2.*ran1(idum)-1.
+ v2=2.*ran1(idum)-1.
+ rsq=v1**2+v2**2
+ if(rsq.ge.1..or.rsq.eq.0.)goto 1
+ fac=sqrt(-2.*log(rsq)/rsq)
+ gset=v1*fac
+ gasdev=v2*fac
+ iset=1
+ else
+ gasdev=gset
+ iset=0
+ endif
+ return
+ END
diff --git a/test/simplemd/in b/test/simplemd/in
new file mode 100644
index 000000000..75eb5f934
--- /dev/null
+++ b/test/simplemd/in
@@ -0,0 +1,10 @@
+inputfile input.xyz
+outputfile output.xyz
+temperature 0.722
+tstep 0.005
+friction 1
+forcecutoff 2.5
+listcutoff 3.0
+nstep 2000
+nconfig 10 trajectory.xyz
+nstat 10 energies.dat
diff --git a/test/simplemd/input.xyz b/test/simplemd/input.xyz
new file mode 100644
index 000000000..bd0d514ea
--- /dev/null
+++ b/test/simplemd/input.xyz
@@ -0,0 +1,110 @@
+108
+5.0388 5.0388 5.0388
+Ar 0 0 0
+Ar 0.8398 0 0.8398
+Ar 0.8398 0.8398 0
+Ar 0 0.8398 0.8398
+Ar 0 0 1.6796
+Ar 0.8398 0 2.5194
+Ar 0.8398 0.8398 1.6796
+Ar 0 0.8398 2.5194
+Ar 0 0 3.3592
+Ar 0.8398 0 4.199
+Ar 0.8398 0.8398 3.3592
+Ar 0 0.8398 4.199
+Ar 0 1.6796 0
+Ar 0.8398 1.6796 0.8398
+Ar 0.8398 2.5194 0
+Ar 0 2.5194 0.8398
+Ar 0 1.6796 1.6796
+Ar 0.8398 1.6796 2.5194
+Ar 0.8398 2.5194 1.6796
+Ar 0 2.5194 2.5194
+Ar 0 1.6796 3.3592
+Ar 0.8398 1.6796 4.199
+Ar 0.8398 2.5194 3.3592
+Ar 0 2.5194 4.199
+Ar 0 3.3592 0
+Ar 0.8398 3.3592 0.8398
+Ar 0.8398 4.199 0
+Ar 0 4.199 0.8398
+Ar 0 3.3592 1.6796
+Ar 0.8398 3.3592 2.5194
+Ar 0.8398 4.199 1.6796
+Ar 0 4.199 2.5194
+Ar 0 3.3592 3.3592
+Ar 0.8398 3.3592 4.199
+Ar 0.8398 4.199 3.3592
+Ar 0 4.199 4.199
+Ar 1.6796 0 0
+Ar 2.5194 0 0.8398
+Ar 2.5194 0.8398 0
+Ar 1.6796 0.8398 0.8398
+Ar 1.6796 0 1.6796
+Ar 2.5194 0 2.5194
+Ar 2.5194 0.8398 1.6796
+Ar 1.6796 0.8398 2.5194
+Ar 1.6796 0 3.3592
+Ar 2.5194 0 4.199
+Ar 2.5194 0.8398 3.3592
+Ar 1.6796 0.8398 4.199
+Ar 1.6796 1.6796 0
+Ar 2.5194 1.6796 0.8398
+Ar 2.5194 2.5194 0
+Ar 1.6796 2.5194 0.8398
+Ar 1.6796 1.6796 1.6796
+Ar 2.5194 1.6796 2.5194
+Ar 2.5194 2.5194 1.6796
+Ar 1.6796 2.5194 2.5194
+Ar 1.6796 1.6796 3.3592
+Ar 2.5194 1.6796 4.199
+Ar 2.5194 2.5194 3.3592
+Ar 1.6796 2.5194 4.199
+Ar 1.6796 3.3592 0
+Ar 2.5194 3.3592 0.8398
+Ar 2.5194 4.199 0
+Ar 1.6796 4.199 0.8398
+Ar 1.6796 3.3592 1.6796
+Ar 2.5194 3.3592 2.5194
+Ar 2.5194 4.199 1.6796
+Ar 1.6796 4.199 2.5194
+Ar 1.6796 3.3592 3.3592
+Ar 2.5194 3.3592 4.199
+Ar 2.5194 4.199 3.3592
+Ar 1.6796 4.199 4.199
+Ar 3.3592 0 0
+Ar 4.199 0 0.8398
+Ar 4.199 0.8398 0
+Ar 3.3592 0.8398 0.8398
+Ar 3.3592 0 1.6796
+Ar 4.199 0 2.5194
+Ar 4.199 0.8398 1.6796
+Ar 3.3592 0.8398 2.5194
+Ar 3.3592 0 3.3592
+Ar 4.199 0 4.199
+Ar 4.199 0.8398 3.3592
+Ar 3.3592 0.8398 4.199
+Ar 3.3592 1.6796 0
+Ar 4.199 1.6796 0.8398
+Ar 4.199 2.5194 0
+Ar 3.3592 2.5194 0.8398
+Ar 3.3592 1.6796 1.6796
+Ar 4.199 1.6796 2.5194
+Ar 4.199 2.5194 1.6796
+Ar 3.3592 2.5194 2.5194
+Ar 3.3592 1.6796 3.3592
+Ar 4.199 1.6796 4.199
+Ar 4.199 2.5194 3.3592
+Ar 3.3592 2.5194 4.199
+Ar 3.3592 3.3592 0
+Ar 4.199 3.3592 0.8398
+Ar 4.199 4.199 0
+Ar 3.3592 4.199 0.8398
+Ar 3.3592 3.3592 1.6796
+Ar 4.199 3.3592 2.5194
+Ar 4.199 4.199 1.6796
+Ar 3.3592 4.199 2.5194
+Ar 3.3592 3.3592 3.3592
+Ar 4.199 3.3592 4.199
+Ar 4.199 4.199 3.3592
+Ar 3.3592 4.199 4.199
diff --git a/test/simplemd/plumed.dat b/test/simplemd/plumed.dat
new file mode 100644
index 000000000..59fe653f3
--- /dev/null
+++ b/test/simplemd/plumed.dat
@@ -0,0 +1,27 @@
+DISTANCE LABEL=C1 ATOMS=0,1 COMPONENTS
+
+RESTRAINT ...
+ KAPPA=10.0
+ ARG=C1
+ STRIDE=5
+ AT=10.0
+ LABEL=rest
+... RESTRAINT
+
+PRINT ...
+ STRIDE=25
+ ARG=C1,C1.x,C1.y,C1.z,rest.*
+ FILE=COLVAR
+... PRINT
+
+# DEBUG logActivity
+
+FLUSH STRIDE=100
+
+ENDPLUMED
+
+commenti
+
+F::COMBINE LABEL=X ARG=C1.x,C1.y,C1.z COEFFICIENTS=1.0,1.0,1.0 POWERS=2.0,2.0,2.0
+F::COMBINE LABEL=Y ARG=X COEFFICIENTS=1.0 POWERS=0.5
+#RESTRAINT KAPPA=10.0 ARG=Y STRIDE=5 AT=1.0
diff --git a/test/simplemd/ran1.f b/test/simplemd/ran1.f
new file mode 100644
index 000000000..7d9fca515
--- /dev/null
+++ b/test/simplemd/ran1.f
@@ -0,0 +1,27 @@
+ FUNCTION ran1(idum)
+ INTEGER idum,IA,IM,IQ,IR,NTAB,NDIV
+ REAL ran1,AM,EPS,RNMX
+ PARAMETER (IA=16807,IM=2147483647,AM=1./IM,IQ=127773,IR=2836,
+ *NTAB=32,NDIV=1+(IM-1)/NTAB,EPS=1.2e-7,RNMX=1.-EPS)
+ INTEGER j,k,iv(NTAB),iy
+ SAVE iv,iy
+ DATA iv /NTAB*0/, iy /0/
+ if (idum.le.0.or.iy.eq.0) then
+ idum=max(-idum,1)
+ do 11 j=NTAB+8,1,-1
+ k=idum/IQ
+ idum=IA*(idum-k*IQ)-IR*k
+ if (idum.lt.0) idum=idum+IM
+ if (j.le.NTAB) iv(j)=idum
+11 continue
+ iy=iv(1)
+ endif
+ k=idum/IQ
+ idum=IA*(idum-k*IQ)-IR*k
+ if (idum.lt.0) idum=idum+IM
+ j=1+iy/NDIV
+ iy=iv(j)
+ iv(j)=idum
+ ran1=min(AM*iy,RNMX)
+ return
+ END
diff --git a/test/simplemd/routines.f90 b/test/simplemd/routines.f90
new file mode 100644
index 000000000..c132a8aa9
--- /dev/null
+++ b/test/simplemd/routines.f90
@@ -0,0 +1,396 @@
+module routines
+implicit none
+contains
+subroutine read_input(temperature,tstep,friction, &
+ forcecutoff,listcutoff,nstep,&
+ nconfig,nstat, &
+ wrapatoms, &
+ inputfile,outputfile,trajfile,statfile, &
+ maxneighbours,idum)
+ implicit none
+ real, intent(out) :: temperature
+ real, intent(out) :: tstep
+ real, intent(out) :: friction
+ real, intent(out) :: forcecutoff
+ real, intent(out) :: listcutoff
+ integer, intent(out) :: nstep
+ integer, intent(out) :: nconfig
+ integer, intent(out) :: nstat
+ logical, intent(out) :: wrapatoms
+ integer, intent(out) :: maxneighbours
+ character(256), intent(out) :: inputfile
+ character(256), intent(out) :: outputfile
+ character(256), intent(out) :: trajfile
+ character(256), intent(out) :: statfile
+ integer, intent(out) :: idum
+ integer :: iostat
+ character(256) :: line,keyword,keyword1
+ integer :: i
+ logical :: foundsharp
+! default values
+ temperature=1.0
+ tstep=0.005
+ friction=0.0
+ forcecutoff=2.5
+ listcutoff=3.0
+ nstep=1
+ nconfig=10
+ nstat=1
+ maxneighbours=1000
+ idum=0
+ wrapatoms=.false.
+ statfile=""
+ trajfile=""
+ outputfile=""
+ inputfile=""
+
+ do
+ read(*,"(a)",iostat=iostat) line
+! when the file finishes, exit the loop
+ if(iostat/=0) exit
+! delete everything past an eventual "#" comment
+ foundsharp=.false.
+ do i=1,len(line)
+ if(line(i:i)=="#") foundsharp=.true.
+ if(foundsharp) line(i:i)=" "
+ end do
+! if the remaining line is empty, skip it
+ if(len_trim(line)==0) cycle
+! read the first word from line
+ read(line,*) keyword
+! the second word is then read to the proper variable
+ select case(keyword)
+ case("temperature")
+ read(line,*) keyword1,temperature
+ case("tstep")
+ read(line,*) keyword1,tstep
+ case("friction")
+ read(line,*) keyword1,friction
+ case("forcecutoff")
+ read(line,*) keyword1,forcecutoff
+ case("listcutoff")
+ read(line,*) keyword1,listcutoff
+ case("nstep")
+ read(line,*) keyword1,nstep
+ case("nconfig")
+ read(line,*) keyword1,nconfig,trajfile
+ case("nstat")
+ read(line,*) keyword1,nstat,statfile
+ case("maxneighbours")
+ read(line,*) keyword1,maxneighbours
+ case("wrapatoms")
+ read(line,*) keyword1,wrapatoms
+ case("inputfile")
+ read(line,*) keyword1,inputfile
+ case("outputfile")
+ read(line,*) keyword1,outputfile
+ case("seed")
+ read(line,*) keyword1,idum
+ idum=-idum ! idum for ran1() needs to be negative
+ case default
+! an unknown word will stop the execution
+ write(0,*) "Unknown keyword :",trim(keyword)
+ stop
+ end select
+ end do
+ if(inputfile=="") then
+ write(0,*) "Specify input file"
+ stop
+ end if
+ if(outputfile=="") then
+ write(0,*) "Specify output file"
+ stop
+ end if
+ if(trajfile=="") then
+ write(0,*) "Specify traj file"
+ stop
+ end if
+ if(statfile=="") then
+ write(0,*) "Specify stat file"
+ stop
+ end if
+end subroutine read_input
+
+subroutine read_positions(inputfile,natoms,positions,cell)
+! read positions and cell from a file called inputfile
+! natoms (input variable) and number of atoms in the file should be consistent
+ implicit none
+ character(*), intent(in) :: inputfile
+ integer, intent(in) :: natoms
+ real, intent(out) :: positions(3,natoms)
+ real, intent(out) :: cell(3)
+ integer :: iatom
+ character(100) :: atomname
+ open(10,file=inputfile)
+ read(10,*)
+ read(10,*) cell
+ do iatom=1,natoms
+ read(10,*) atomname,positions(:,iatom)
+ end do
+! note: atomname is read but not used
+ close(10)
+end subroutine read_positions
+
+subroutine read_natoms(inputfile,natoms)
+! read the number of atoms in file "input.xyz"
+ implicit none
+ character(*), intent(in) :: inputfile
+ integer, intent(out):: natoms
+ open(10,file=inputfile)
+ read(10,*) natoms
+ close(10)
+end subroutine read_natoms
+
+subroutine write_positions(trajfile,natoms,positions,cell,wrapatoms)
+! write positions on file trajfile
+! positions are appended at the end of the file
+ implicit none
+ character(*), intent(in) :: trajfile
+ integer, intent(in) :: natoms
+ real, intent(in) :: positions(3,natoms)
+ real, intent(in) :: cell(3)
+ logical, intent(in) :: wrapatoms
+ integer :: iatom
+ real :: pos(3)
+ logical, save :: first=.true.
+ if(first) then
+ open(10,file=trajfile)
+ first=.false.
+ else
+ open(10,file=trajfile,position="append")
+ end if
+ write(10,*) natoms
+ write(10,*) cell
+ do iatom=1,natoms
+! usually, it is better not to apply pbc here, so that diffusion
+! is more easily calculated from a trajectory file:
+ if(wrapatoms) then
+ call pbc(cell,positions(:,iatom),pos)
+ else
+ pos=positions(:,iatom)
+ end if
+ write(10,*) "Ar",pos
+ end do
+ close(10)
+end subroutine write_positions
+
+subroutine write_final_positions(outputfile,natoms,positions,cell,wrapatoms)
+! write positions on file outputfile
+ character(*), intent(in) :: outputfile
+ integer, intent(in) :: natoms
+ real, intent(in) :: positions(3,natoms)
+ real, intent(in) :: cell(3)
+ logical, intent(in) :: wrapatoms
+ integer :: iatom
+ real :: pos(3)
+ open(10,file=outputfile)
+ write(10,*) natoms
+ write(10,*) cell
+ do iatom=1,natoms
+! usually, it is better not to apply pbc here, so that diffusion
+! is more easily calculated from a trajectory file:
+ if(wrapatoms) then
+ call pbc(cell,positions(:,iatom),pos)
+ else
+ pos=positions(:,iatom)
+ end if
+ write(10,*) "Ar",pos
+ end do
+ close(10)
+end subroutine write_final_positions
+
+subroutine write_statistics(statfile,istep,tstep,natoms,engkin,engconf,engint)
+! write statistics on file statfile
+ character(*), intent(in) :: statfile
+ integer, intent(in) :: istep
+ real, intent(in) :: tstep
+ integer, intent(in) :: natoms
+ real, intent(in) :: engkin
+ real, intent(in) :: engconf
+ real, intent(in) :: engint
+ logical, save :: first=.true.
+ integer, save :: last_time_reopened=0
+ if(first) then
+! first time this routine is called, open the file
+ open(666,file=statfile)
+ first=.false.
+ end if
+ if(istep-last_time_reopened>100) then
+! every 100 steps, reopen the file to flush the buffer
+ close(666)
+ open(666,file=statfile,position="append")
+ last_time_reopened=istep
+ end if
+ write(666,"(i10,99g13.6)") istep,istep*tstep,2.0*engkin/(3.0*natoms),engconf,engkin+engconf,engkin+engconf+engint
+end subroutine write_statistics
+
+subroutine randomize_velocities(natoms,temperature,masses,velocities,idum)
+! randomize the velocities according to the temperature
+ implicit none
+ integer, intent(in) :: natoms
+ real, intent(in) :: temperature
+ real, intent(in) :: masses(natoms)
+ real, intent(out) :: velocities(3,natoms)
+ integer, intent(inout) :: idum
+ real, external :: gasdev
+ integer :: iatom,i
+ do iatom=1,natoms
+ do i=1,3
+ velocities(i,iatom)=sqrt(temperature/masses(iatom))*gasdev(idum)
+ end do
+ end do
+end subroutine randomize_velocities
+
+subroutine compute_engkin(natoms,masses,velocities,engkin)
+! calculate the kinetic energy from the velocities
+ implicit none
+ integer, intent(in) :: natoms
+ real, intent(in) :: masses(natoms)
+ real, intent(in) :: velocities(3,natoms)
+ real, intent(out):: engkin
+ integer :: iatom
+ engkin=0.0
+ do iatom=1,natoms
+ engkin=engkin+0.5*masses(iatom)*sum(velocities(:,iatom)**2)
+ end do
+end subroutine compute_engkin
+
+subroutine pbc(cell,vin,vout)
+! apply periodic boundary condition to a vector
+ implicit none
+ real, intent(in) :: cell(3)
+ real, intent(in) :: vin(3)
+ real, intent(out) :: vout(3)
+ integer :: i
+ do i=1,3
+ vout(i)=vin(i)-nint(vin(i)/cell(i))*cell(i)
+ end do
+end subroutine pbc
+
+subroutine check_list(natoms,positions,positions0,listcutoff,forcecutoff,recompute)
+! check if the neighbour list have to be recomputed
+ implicit none
+ integer, intent(in) :: natoms
+ real, intent(in) :: positions(3,natoms)
+ real, intent(in) :: positions0(3,natoms)
+ real, intent(in) :: listcutoff
+ real, intent(in) :: forcecutoff
+ logical, intent(out) :: recompute
+ real :: displacement(3) ! displacement from positions0 to positions
+ real :: delta2 ! square of the 'skin' thickness
+ integer :: iatom
+ recompute=.false.
+ delta2=(0.5*(listcutoff-forcecutoff))**2
+! if ANY atom moved more than half of the skin thickness, recompute is set to .true.
+ do iatom=1,natoms
+ displacement=positions(:,iatom)-positions0(:,iatom)
+ if(sum(displacement**2)>delta2) recompute=.true.
+ end do
+end subroutine check_list
+
+subroutine compute_list(natoms,listsize,positions,cell,listcutoff,point,list)
+ implicit none
+ integer, intent(in) :: natoms
+ integer, intent(in) :: listsize
+ real, intent(in) :: positions(3,natoms)
+ real, intent(in) :: cell(3)
+ real, intent(in) :: listcutoff
+! see Allen-Tildesey for a definition of point and list
+ integer, intent(out) :: point(natoms)
+ integer, intent(out) :: list(listsize)
+ integer :: iatom,jatom ! indexes of the two involved atoms
+ real :: distance(3) ! distance of the two atoms
+ real :: distance_pbc(3) ! minimum-image distance of the two atoms
+ real :: listcutoff2 ! squared list cutoff
+ listcutoff2=listcutoff**2
+ point(1)=1
+ do iatom=1,natoms-1
+ point(iatom+1)=point(iatom)
+ do jatom=iatom+1,natoms
+ distance=positions(:,iatom)-positions(:,jatom)
+ call pbc(cell,distance,distance_pbc)
+! if the interparticle distance is larger than the cutoff, skip
+ if(sum(distance_pbc**2)>listcutoff2) cycle
+ if(point(iatom+1)>listsize) then
+! too many neighbours
+ write(0,*) "Verlet list size exceeded"
+ write(0,*) "Increase maxneighbours"
+ stop
+ end if
+ list(point(iatom+1))=jatom
+ point(iatom+1)=point(iatom+1)+1
+ end do
+ end do
+end subroutine compute_list
+
+subroutine compute_forces(natoms,listsize,positions,cell,forcecutoff,point,list,forces,engconf)
+ implicit none
+ integer, intent(in) :: natoms
+ integer, intent(in) :: listsize
+ real, intent(in) :: positions(3,natoms)
+ real, intent(in) :: cell(3)
+ real, intent(in) :: forcecutoff
+ integer, intent(in) :: point(natoms)
+ integer, intent(in) :: list(listsize)
+ real, intent(out) :: forces(3,natoms)
+ real, intent(out) :: engconf
+ integer :: iatom,jatom ! indexes of the two involved atoms
+ integer :: jlist ! counter for the neighbours of iatom
+ real :: distance(3) ! distance of the two atoms
+ real :: distance_pbc(3) ! minimum-image distance of the two atoms
+ real :: distance_pbc2 ! squared minimum-image distance
+ real :: forcecutoff2 ! squared force cutoff
+ real :: f(3) ! force
+ real :: engcorrection ! energy necessary shift the potential avoiding discontinuities
+ forcecutoff2=forcecutoff**2
+ engconf=0.0
+ forces=0.0
+ engcorrection=4.0*(1.0/forcecutoff2**6-1.0/forcecutoff2**3)
+ do iatom=1,natoms-1
+ do jlist=point(iatom),point(iatom+1)-1
+ jatom=list(jlist)
+ distance=positions(:,iatom)-positions(:,jatom)
+ call pbc(cell,distance,distance_pbc)
+ distance_pbc2=sum(distance_pbc**2)
+! if the interparticle distance is larger than the cutoff, skip
+ if(distance_pbc2>forcecutoff2) cycle
+ engconf=engconf+4.0*(1.0/distance_pbc2**6-1.0/distance_pbc2**3)-engcorrection
+ f=2.0*distance_pbc*4.0*(6.0/distance_pbc2**7-3.0/distance_pbc2**4)
+! same force on the two atoms, with opposite sign:
+ forces(:,iatom)=forces(:,iatom)+f
+ forces(:,jatom)=forces(:,jatom)-f
+ end do
+ end do
+end subroutine compute_forces
+
+subroutine thermostat(natoms,masses,dt,friction,temperature,velocities,engint,idum)
+! Langevin thermostat, implemented as decribed in Bussi and Parrinello, Phys. Rev. E (2007)
+! it is a linear combination of old velocities and new, randomly chosen, velocity,
+! with proper coefficients
+ implicit none
+ integer, intent(in) :: natoms
+ real, intent(in) :: masses(natoms)
+ real, intent(in) :: dt
+ real, intent(in) :: friction
+ real, intent(in) :: temperature
+ real, intent(inout) :: velocities(3,natoms)
+ real, intent(inout) :: engint ! contribution of phase-space compression
+ ! its increment is equal to minus the kinetic-energy increment due to the
+ ! thermostat
+ integer, intent(inout) :: idum
+ real :: c1 ! coefficient for the old velocity
+ real :: c2 ! coefficient for the new velocity
+ real, external :: gasdev
+ integer :: i,iatom
+ c1=exp(-friction*dt)
+ do iatom=1,natoms
+ c2=sqrt((1.0-c1**2)*temperature/masses(iatom))
+ do i=1,3
+ engint=engint+0.5*masses(iatom)*velocities(i,iatom)**2
+ velocities(i,iatom)=c1*velocities(i,iatom)+c2*gasdev(idum)
+ engint=engint-0.5*masses(iatom)*velocities(i,iatom)**2
+ end do
+ end do
+end subroutine thermostat
+end module routines
+
diff --git a/test/simplemd/simplemd.f90 b/test/simplemd/simplemd.f90
new file mode 100644
index 000000000..a7beba17d
--- /dev/null
+++ b/test/simplemd/simplemd.f90
@@ -0,0 +1,204 @@
+
+program simplemd
+use routines
+implicit none
+
+integer :: natoms ! number of atoms
+real, allocatable :: positions(:,:) ! atomic positions
+real, allocatable :: velocities(:,:) ! velocities
+ ! was calculated last time
+real, allocatable :: masses(:) ! masses
+real, allocatable :: forces(:,:) ! forces
+real :: cell(3) ! cell size
+real :: cell9(9) ! cell size
+
+! neighbour list variables
+! see Allen and Tildesey book for details
+integer :: listsize ! size of the list array
+integer, allocatable :: list(:) ! neighbour list
+integer, allocatable :: point(:) ! pointer to neighbour list
+real, allocatable :: positions0(:,:) ! reference atomic positions, i.e. positions when the neighbour list
+
+! input parameters
+! all of them have a reasonable default value, set in read_input()
+real :: tstep ! simulation timestep
+real :: temperature ! temperature
+real :: friction ! friction for Langevin dynamics (for NVE, use 0)
+real :: listcutoff ! cutoff for neighbour list
+real :: forcecutoff ! cutoff for forces
+integer :: nstep ! number of steps
+integer :: nconfig ! stride for output of configurations
+integer :: nstat ! stride for output of statistics
+integer :: maxneighbour ! maximum average number of neighbours per atom
+integer :: idum ! seed
+logical :: wrapatoms ! if true, atomic coordinates are written wrapped in minimal cell
+character(256) :: inputfile ! name of file with starting configuration (xyz)
+character(256) :: outputfile ! name of file with final configuration (xyz)
+character(256) :: trajfile ! name of the trajectory file (xyz)
+character(256) :: statfile ! name of the file with statistics
+
+
+real :: engkin ! kinetic energy
+real :: engconf ! configurational energy
+real :: engint ! integral for conserved energy in Langevin dynamics
+
+logical :: recompute_list ! control if the neighbour list have to be recomputed
+integer :: istep ! step counter
+integer :: iatom
+
+logical :: plumed
+integer :: plumedavailable
+
+CALL plumed_installed(plumedavailable)
+
+plumed=.false.
+if(plumedavailable>0)plumed=.true.
+
+IF(plumed) THEN
+ CALL plumed_g_create()
+END IF
+
+call read_input(temperature,tstep,friction,forcecutoff, &
+ listcutoff,nstep,nconfig,nstat, &
+ wrapatoms, &
+ inputfile,outputfile,trajfile,statfile, &
+ maxneighbour,idum)
+
+! number of atoms is read from file inputfile
+call read_natoms(inputfile,natoms)
+
+! write the parameters in output so they can be checked
+write(*,*) "Starting configuration : ",trim(inputfile)
+write(*,*) "Final configuration : ",trim(outputfile)
+write(*,*) "Number of atoms : ",natoms
+write(*,*) "Temperature : ",temperature
+write(*,*) "Time step : ",tstep
+write(*,*) "Friction : ",friction
+write(*,*) "Cutoff for forces : ",forcecutoff
+write(*,*) "Cutoff for neighbour list : ",listcutoff
+write(*,*) "Number of steps : ",nstep
+write(*,*) "Stride for trajectory : ",nconfig
+write(*,*) "Trajectory file : ",trim(trajfile)
+write(*,*) "Stride for statistics : ",nstat
+write(*,*) "Statistics file : ",trim(statfile)
+write(*,*) "Max average number of neighbours : ",maxneighbour
+write(*,*) "Seed : ",idum
+write(*,*) "Are atoms wrapped on output? : ",wrapatoms
+
+! Since each atom pair is counted once, the total number of pairs
+! will be half of the number of neighbours times the number of atoms
+listsize=maxneighbour*natoms/2
+
+! allocation of dynamical arrays
+allocate(positions(3,natoms))
+allocate(positions0(3,natoms))
+allocate(velocities(3,natoms))
+allocate(forces(3,natoms))
+allocate(masses(natoms))
+allocate(point(natoms))
+allocate(list(listsize))
+
+
+! masses are hard-coded to 1
+masses=1.0
+
+! energy integral initialized to 0
+engint=0.0
+
+! positions are read from file inputfile
+call read_positions(inputfile,natoms,positions,cell)
+
+! velocities are randomized according to temperature
+call randomize_velocities(natoms,temperature,masses,velocities,idum)
+
+!CALL init_metadyn(natoms,tstep,masses,masses,1,1.0D0,"plumed.dat"//char(0));
+IF(plumed) THEN
+ CALL plumed_g_cmd("setNatoms"//char(0),natoms)
+ CALL plumed_g_cmd("setMDEngine"//char(0),"simplemd"//char(0))
+ CALL plumed_g_cmd("setTimestep"//char(0),tstep)
+ CALL plumed_g_cmd("setPlumedDat"//char(0),"plumed.dat"//char(0))
+ CALL plumed_g_cmd("init"//char(0))
+ENDIF
+
+
+! neighbour list are computed, and reference positions are saved
+call compute_list(natoms,listsize,positions,cell,listcutoff,point,list)
+write(*,*) "List size: ",point(natoms)-1
+positions0=positions
+
+! forces are computed before starting md
+call compute_forces(natoms,listsize,positions,cell,forcecutoff,point,list,forces,engconf)
+
+! here is the main md loop
+! Langevin thermostat is applied before and after a velocity-Verlet integrator
+! the overall structure is:
+! thermostat
+! update velocities
+! update positions
+! (eventually recompute neighbour list)
+! compute forces
+! update velocities
+! thermostat
+! (eventually dump output informations)
+do istep=1,nstep
+ call thermostat(natoms,masses,0.5*tstep,friction,temperature,velocities,engint,idum)
+
+ do iatom=1,natoms
+ velocities(:,iatom)=velocities(:,iatom)+forces(:,iatom)*0.5*tstep/masses(iatom)
+ end do
+
+ do iatom=1,natoms
+ positions(:,iatom)=positions(:,iatom)+velocities(:,iatom)*tstep
+ end do
+
+! a check is performed to decide whether to recalculate the neighbour list
+ call check_list(natoms,positions,positions0,listcutoff,forcecutoff,recompute_list)
+ if(recompute_list) then
+ call compute_list(natoms,listsize,positions,cell,listcutoff,point,list)
+ positions0=positions
+ write(*,*) "Neighbour list recomputed at step ",istep
+ write(*,*) "List size: ",point(natoms)-1
+ end if
+
+ call compute_forces(natoms,listsize,positions,cell,forcecutoff,point,list,forces,engconf)
+! forces=0.0
+IF(plumed) THEN
+ CALL plumed_g_cmd("setMasses"//char(0),masses)
+ CALL plumed_g_cmd("setForces"//char(0),forces)
+ CALL plumed_g_cmd("setStep"//char(0),istep)
+ CALL plumed_g_cmd("setPositions"//char(0),positions)
+ CALL plumed_g_cmd("calc"//char(0),0)
+ENDIF
+
+ do iatom=1,natoms
+ velocities(:,iatom)=velocities(:,iatom)+forces(:,iatom)*0.5*tstep/masses(iatom)
+ end do
+
+ call thermostat(natoms,masses,0.5*tstep,friction,temperature,velocities,engint,idum)
+
+! kinetic energy is calculated
+ call compute_engkin(natoms,masses,velocities,engkin)
+
+! eventually, write positions and statistics
+ if(modulo(istep,nconfig)==0) call write_positions(trajfile,natoms,positions,cell,wrapatoms)
+ if(modulo(istep,nstat)==0) call write_statistics(statfile,istep,tstep,natoms,engkin,engconf,engint)
+
+end do
+
+call write_final_positions(outputfile,natoms,positions,cell,wrapatoms)
+write(*,*) "Execution completed"
+
+! deallocation of all allocatable array
+deallocate(positions)
+deallocate(velocities)
+deallocate(forces)
+deallocate(masses)
+deallocate(positions0)
+deallocate(point)
+deallocate(list)
+
+IF(plumed) THEN
+ CALL plumed_g_finalize()
+END IF
+
+end program simplemd
diff --git a/tools/plumed b/tools/plumed
new file mode 100755
index 000000000..2729175a5
--- /dev/null
+++ b/tools/plumed
@@ -0,0 +1,71 @@
+#! /bin/bash
+
+MANUAL="\
++++ PLUMED tool +++
+
+Actions (choose only one):
+ help
+ print this help and exit
+ patch
+ patch an MD code (patch -h for help)
+ newcv
+ create a new collective variable from a template (newcv -h for help)
+Options:
+ --root ROOT
+ set path to plumed directory (default: PLUMED_ROOT environment variable)
+"
+
+prefix=""
+action=""
+
+exitloop=""
+
+while [ -n "$*" ]
+do
+
+ prefix_option="$prefix$1"
+ prefix=""
+
+ case "$prefix_option" in
+ (help|--help|-h) echo "$MANUAL" ; exit ;;
+ (patch) action=patch; exitloop=yes ;;
+ (newcv) action=newcv; exitloop=yes ;;
+ (--root=*) PLUMED_ROOT="${prefix_option#--root=}" ;;
+ (*)
+ echo "ERROR: Unknown option $prefix_option. Use 'plumed help' for help"
+ exit
+ esac
+ shift
+
+ test -n "$exitloop" && break
+done
+
+if [ -z "$action" ] ; then
+ echo "Nothing to do. Use 'plumed help' for help"
+ exit
+fi
+
+echo "PLUMED tool"
+echo
+if [ -z "$PLUMED_ROOT" ]
+then
+ echo "ERROR: I cannot find PLUMED"
+ echo "Please set PLUMED_ROOT environment variable or use --root"
+ exit
+fi
+if [ ! -d "$PLUMED_ROOT/patches/" ]
+then
+ echo "ERROR: cannot find $PLUMED_ROOT/patches/ directory"
+ echo "Check your PLUMED_ROOT variable or --root option"
+ exit
+fi
+
+export PLUMED_ROOT
+
+case "$action" in
+ (patch) ${PLUMED_ROOT}/patches/patch.sh "$@" ;;
+ (newcv) ${PLUMED_ROOT}/tools/scripts/newcv.sh "$@" ;;
+esac
+
+
+
diff --git a/tools/scripts/newcv.sh b/tools/scripts/newcv.sh
new file mode 100755
index 000000000..02c3e7d62
--- /dev/null
+++ b/tools/scripts/newcv.sh
@@ -0,0 +1,16 @@
+#! /bin/bash
+
+if [ $# != 2 ] ;
+then
+ echo "ERROR"
+ echo "type 'plumed newcv directive cvname'"
+ echo "E.g. 'plumed newcv TORSION Torsion'"
+ exit 1
+fi
+
+directive=$1
+cvname=$2
+
+sed "s/TEMPLATE/$directive/g
+ s/Template/$cvname/g" $PLUMED_ROOT/src/ColvarTemplate.cpp > Colvar${cvname}.cpp
+
diff --git a/user-doc/.gitignore b/user-doc/.gitignore
new file mode 100644
index 000000000..628872b9e
--- /dev/null
+++ b/user-doc/.gitignore
@@ -0,0 +1,6 @@
+/html
+/latex
+/*.tmp
+/DocPostproc.txt
+/automatic
+
diff --git a/user-doc/Doc.txt b/user-doc/Doc.txt
new file mode 100644
index 000000000..2b779464e
--- /dev/null
+++ b/user-doc/Doc.txt
@@ -0,0 +1,176 @@
+/**
+\mainpage User guide
+
+Introduction
+
+\section WhatsNew What's new
+
+\subsection NewInputSyntax New syntax for the input file
+
+Briefly describe the difference between old and new input
+
+\subsection NewFeatures List of new features
+
+List of new features
+
+\section Topics
+
+\subpage Installation
+
+\subpage BasicUsage
+
+\subpage AdvancedTopics
+
+\subpage Tools
+
+\page Reference
+
+List of directives to manipulate input: \subpage InputDirectives
+
+List of collective variables: \subpage Colvar
+
+List of functions: \subpage Function
+
+List of free energy methods: \subpage Bias
+
+List of general purpose directives: \subpage GenericDirectives
+
+\page Installation
+
+\section CompilingPlumed Compiling Plumed
+
+How to configure
+
+How to compile
+
+\section Patching Patching your MD code
+
+\section Testing Testing the installation
+
+\section InstallingPlumedOnAMainframe Installing Plumed on a mainframe
+
+Notes on shared libraries, modules, etc.
+
+\page BasicUsage Basic usage
+
+\section HowToActivatePlumed How to activate Plumed
+
+\section TheInputFile The input file
+
+Directives
+
+Continued lines
+
+Labeling the directives
+
+Units (see \ref UNITS).
+
+\section MonitoringSimulationsI Monitoring simulations I: Collective variables
+
+Example with \ref DISTANCE and \ref PRINT
+
+For more collective variables, see \ref Colvar
+
+\section MonitoringSimulationsII Monitoring simulations II: Functions
+
+Example with \ref COMBINE
+
+For more, see \ref Function
+
+\section BiasingSimulations Biasing simulations
+
+Example with \ref RESTRAINT
+
+For more, see \ref Bias
+
+\page AdvancedTopics Advanced topics
+
+\section AdvancedInput Advanced input file
+
+Inclusion of other files
+
+Loading libraries
+
+\section AtomGroups Atom groups
+
+\section AtomAlignment Atom alignement
+
+\section ReplicaExchange Replica exchange
+
+Discuss the way input is provided.
+A different bias is allowed on the different replicas.
+
+\page Tools
+
+\page InputDirectives Input directives
+
+These are directives which can be used to manipulate the input file.
+
+\section Comments
+
+\section ContinuationLines Continuation lines
+
+\section INCLUDE
+
+\section LOAD
+
+\section ENDPLUMED
+
+\page Colvar Collective Variables
+
+\attention This page should be automatically generated from the .cpp files
+
+@COLVAR@
+
+\page Function Functions
+
+The following keywords are available for all directives of this section:
+- ARG:
+ This keyword is used to specify on which variables the function is computed
+ It is a comma-separated list of labels. Here is an example with \ref COMBINE
+\verbatim
+DISTANCE ATOMS=1,5 LABEL=d1
+DISTANCE ATOMS=2,6 LABEL=d2
+COMBINE ARG=d1,d2 POWERS=2
+\endverbatim
+
+\attention This page should be automatically generated from the .cpp files
+
+@FUNCTION@
+
+\page Bias
+
+The following keywords are available for all directives of this section:
+
+- ARG:
+ This keyword is used to specify on which variables the bias is acting.
+ It is a comma-separated list of labels. Here is an example with \ref RESTRAINT
+\verbatim
+DISTANCE ATOMS=1,5 LABEL=d1
+DISTANCE ATOMS=2,6 LABEL=d2
+RESTRAINT ARG=d1,d2 AT=5.0,6.0 KAPPA=100.0,50.0
+\endverbatim
+- STRIDE:
+ PLUMED implements a multiple-time-step scheme. Using the keyword STRIDE
+ one can set how frequently the bias should be applied, in units of time steps.
+ It can be used to decrease the impact of variables which are computationally heavy.
+ Here is an example with \ref RESTRAINT
+\verbatim
+DISTANCE ATOMS=1,5 LABEL=d1
+RESTRAINT ARG=d1 AT=5.0 KAPPA=100.0 STRIDE=2
+\endverbatim
+
+\attention This page should be automatically generated from the .cpp files
+
+@BIAS@
+
+\page GenericDirectives Generic directives
+
+\attention The following pages should be automatically generated from the .cpp files
+
+@GENERIC@
+
+
+
+*/
+
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
new file mode 100644
index 000000000..d119df1d3
--- /dev/null
+++ b/user-doc/Doxyfile
@@ -0,0 +1,1649 @@
+# Doxyfile 1.7.2
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+PROJECT_NAME = "A PLUMED CLONE"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY =
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip.
+
+STRIP_FROM_PATH =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful if your file system
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 8
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it
+# parses. With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this
+# tag. The format is ext=language, where ext is a file extension, and language
+# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
+# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
+# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
+# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
+# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also makes the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default)
+# will make doxygen replace the get and set methods by a property in the
+# documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING = YES
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penality.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will roughly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespaces are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = NO
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
+# will sort the (brief and detailed) documentation of class members so that
+# constructors and destructors are listed first. If set to NO (the default)
+# the constructors will appear in the respective orders defined by
+# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
+# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
+# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or macro consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and macros in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page. This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
+# by doxygen. The layout file controls the global structure of the generated
+# output files in an output format independent way. The create the layout file
+# that represents doxygen's defaults, run doxygen with the -l option.
+# You can optionally specify a file name after the option, if omitted
+# DoxygenLayout.xml will be used as the name of the layout file.
+
+LAYOUT_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# The WARN_NO_PARAMDOC option can be enabled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = DocPostproc.txt
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
+# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
+# *.f90 *.f *.vhd *.vhdl
+
+FILE_PATTERNS =
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# directories that are symbolic links (a Unix filesystem feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output. If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis. Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match. The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
+# is applied to all files.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code. Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET =
+
+# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
+# Doxygen will adjust the colors in the stylesheet and background images
+# according to this color. Hue is specified as an angle on a colorwheel,
+# see http://en.wikipedia.org/wiki/Hue for more information.
+# For instance the value 0 represents red, 60 is yellow, 120 is green,
+# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
+# The allowed range is 0 to 359.
+
+HTML_COLORSTYLE_HUE = 220
+
+# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
+# the colors in the HTML output. For a value of 0 the output will use
+# grayscales only. A value of 255 will produce the most vivid colors.
+
+HTML_COLORSTYLE_SAT = 100
+
+# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
+# the luminance component of the colors in the HTML output. Values below
+# 100 gradually make the output lighter, whereas values above 100 make
+# the output darker. The value divided by 100 is the actual gamma applied,
+# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
+# and 100 does not change the gamma.
+
+HTML_COLORSTYLE_GAMMA = 80
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP = YES
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
+# for more information.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
+# the documentation publisher. This should be a reverse domain-name style
+# string, e.g. com.mycompany.MyDocSet.documentation.
+
+DOCSET_PUBLISHER_ID = org.doxygen.Publisher
+
+# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
+
+DOCSET_PUBLISHER_NAME = Publisher
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
+# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
+# that can be used as input for Qt's qhelpgenerator to generate a
+# Qt Compressed Help (.qch) of the generated HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
+# add. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
+# custom filter to add. For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
+# Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
+# project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
+# Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+# will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
+# the help appears.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = NO
+
+# This tag can be used to set the number of enum values (range [0,1..20])
+# that doxygen will group on one line in the generated HTML documentation.
+# Note that a value of 0 will completely suppress the enum values from
+# appearing in the overview section.
+
+ENUM_VALUES_PER_LINE = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to YES, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW = YES
+
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+USE_INLINE_TREES = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 200
+
+# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
+# links to external symbols imported via tag files in a separate window.
+
+EXT_LINKS_IN_WINDOW = NO
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+# Use the FORMULA_TRANPARENT tag to determine whether or not the images
+# generated for formulas are transparent PNGs. Transparent PNGs are
+# not supported properly for IE 6.0, but are supported on all modern browsers.
+# Note that when changing this option you need to delete any form_*.png files
+# in the HTML output before the changes have effect.
+
+FORMULA_TRANSPARENT = YES
+
+# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
+# (see http://www.mathjax.org) which uses client side Javascript for the
+# rendering instead of using prerendered bitmaps. Use this if you do not
+# have LaTeX installed or if you want to formulas look prettier in the HTML
+# output. When enabled you also need to install MathJax separately and
+# configure the path to it using the MATHJAX_RELPATH option.
+
+USE_MATHJAX = NO
+
+# When MathJax is enabled you need to specify the location relative to the
+# HTML output directory using the MATHJAX_RELPATH option. The destination
+# directory should contain the MathJax.js script. For instance, if the mathjax
+# directory is located at the same level as the HTML output directory, then
+# MATHJAX_RELPATH should be ../mathjax. The default value points to the
+# mathjax.org site, so you can quickly see the result without installing
+# MathJax, but it is strongly recommended to install a local copy of MathJax
+# before deployment.
+
+MATHJAX_RELPATH = http://www.mathjax.org/mathjax
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box
+# for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using
+# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
+# (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE = NO
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
+# implemented using a PHP enabled web server instead of at the web client
+# using Javascript. Doxygen will generate the search PHP script and index
+# file to put on the web server. The advantage of the server
+# based approach is that it scales better to large projects and allows
+# full text search. The disadvantages are that it is more difficult to setup
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include
+# source code with syntax highlighting in the LaTeX output.
+# Note that which sources are shown also depends on other settings
+# such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader. This is useful
+# if you want to understand what is going on. On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all function-like macros that are alone
+# on a line, have an all uppercase name, and do not end with a semicolon. Such
+# function macros are typically used for boiler-plate code, and will confuse
+# the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# this location is as follows:
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths or
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option also works with HAVE_DOT disabled, but it is recommended to
+# install and use dot, since it yields more powerful graphs.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = NO
+
+# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
+# allowed to run in parallel. When set to 0 (the default) doxygen will
+# base this on the number of processors available in the system. You can set it
+# explicitly to a value larger than 0 to get control over the balance
+# between CPU load and processing speed.
+
+DOT_NUM_THREADS = 0
+
+# By default doxygen will write a font called FreeSans.ttf to the output
+# directory and reference it in all dot files that doxygen generates. This
+# font does not include all possible unicode characters however, so when you need
+# these (or just want a differently looking font) you can specify the font name
+# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the output directory to look for the
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a
+# different font using DOT_FONTNAME you can set the path where dot
+# can find it using this tag.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will generate a graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are png, jpg, or gif.
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The MSCFILE_DIRS tag can be used to specify one or more directories that
+# contain msc files that are included in the documentation (see the
+# \mscfile command).
+
+MSCFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = YES
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
diff --git a/user-doc/Makefile b/user-doc/Makefile
new file mode 100644
index 000000000..e41a54dae
--- /dev/null
+++ b/user-doc/Makefile
@@ -0,0 +1,9 @@
+
+.PHONY: all clean
+
+all:
+ ./extract
+ doxygen
+
+clean:
+ rm -fr html latex automatic DocPostproc.txt *~
diff --git a/user-doc/extract b/user-doc/extract
new file mode 100755
index 000000000..83fca78cd
--- /dev/null
+++ b/user-doc/extract
@@ -0,0 +1,38 @@
+#! /bin/bash
+mkdir automatic
+
+cat ../src/*cpp |
+awk '{
+ if($1=="//+ENDPLUMEDOC") inside=0;
+ if(inside && $1!="/**" && $1!="*/") print $0 >output
+ if($1=="//+PLUMEDOC"){
+ if($2=="COLVAR" || $2=="FUNCTION" || $2=="BIAS" || $2=="GENERIC"){
+ output="automatic/"$2".txt";
+ print "\\section "$3 > output
+ inside=1;
+ }
+ }
+}'
+
+cat Doc.txt |
+{
+ while read -r LINE ;
+ do
+ if [ "$LINE" = "@COLVAR@" ]
+ then
+ cat automatic/COLVAR.txt
+ elif [ "$LINE" = "@BIAS@" ]
+ then
+ cat automatic/BIAS.txt
+ elif [ "$LINE" = "@FUNCTION@" ]
+ then
+ cat automatic/FUNCTION.txt
+ elif [ "$LINE" = "@GENERIC@" ]
+ then
+ cat automatic/GENERIC.txt
+ else
+ echo -E "$LINE"
+ fi
+ done
+} > DocPostproc.txt
+
--
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