diff --git a/CHANGES/v2.1.txt b/CHANGES/v2.1.txt
index b79211d36e642e54181553b093b0987a725a4151..f3d51a6ec1482e597d61936a3c09595b2afdfbbc 100644
--- a/CHANGES/v2.1.txt
+++ b/CHANGES/v2.1.txt
@@ -80,7 +80,7 @@ character now has a special usage in component names.
the configuration system falls back to an internal version which implements a minimal list
of plugins (gromacs and dcd) (kindly provided by T. Giorgino).
- \ref switchingfunction : added STRETCH flag.
- - Negative strides in atom ranges (e.g. 10-1:-3).
+ - Negative strides in atom ranges (e.g. ATOMS=10-1:-3 is expanded to ATOMS=10,7,4,1).
- \ref COORDINATION and \ref DHENERGY with NLIST now work correctly in replica exchange simulations.
- Multicolvars with neighbor lists now work correctly in replica exchange simulations.
- Improved multicolvar neighbor lists.
diff --git a/patches/namd-2.8.config b/patches/namd-2.8.config
index 991290087a4827c57884b42ffb6e5702961f2eed..c255576a2eef131373bd8245a533c72ffa9764be 100644
--- a/patches/namd-2.8.config
+++ b/patches/namd-2.8.config
@@ -6,7 +6,7 @@ function plumed_preliminary_test(){
}
function plumed_patch_info(){
- echo "WARNING: NAMD does not currently take into account virial contributions"
+ echo "\bug NAMD does not currently take into account virial contributions"
echo "from PLUMED. Please use constant volume simulations only"
echo ""
echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/"
diff --git a/patches/namd-2.9.config b/patches/namd-2.9.config
index 991290087a4827c57884b42ffb6e5702961f2eed..c255576a2eef131373bd8245a533c72ffa9764be 100644
--- a/patches/namd-2.9.config
+++ b/patches/namd-2.9.config
@@ -6,7 +6,7 @@ function plumed_preliminary_test(){
}
function plumed_patch_info(){
- echo "WARNING: NAMD does not currently take into account virial contributions"
+ echo "\bug NAMD does not currently take into account virial contributions"
echo "from PLUMED. Please use constant volume simulations only"
echo ""
echo "For more information on NAMD you should visit http://www.ks.uiuc.edu/Research/namd/"
diff --git a/src/multicolvar/Torsions.cpp b/src/multicolvar/Torsions.cpp
index 9f049f01f793d35953bb2cf75ad9fa9de7959a70..6a8a44fe458e23833344a708997d9e0791a23c2b 100644
--- a/src/multicolvar/Torsions.cpp
+++ b/src/multicolvar/Torsions.cpp
@@ -31,7 +31,7 @@ using namespace std;
namespace PLMD{
namespace multicolvar{
-//+PLUMEDOC COLVAR TORSIONS
+//+PLUMEDOC MCOLVAR TORSIONS
/*
Calculate whether or not a set of torsional angles are within a particular range.
diff --git a/user-doc/Installation.txt b/user-doc/Installation.txt
index 3524a0d42d2aa82d95272d988e5568beec35fb3c..149806206a48837d98d5a5f2b6842c51f459849c 100644
--- a/user-doc/Installation.txt
+++ b/user-doc/Installation.txt
@@ -12,7 +12,7 @@ For those of you who are impatient, the following might do the job:
> ./configure --prefix=/usr/local/lib
> make -j 4
> make doc # this is optional and requires doxygen installed
-> make install
+> make install # this is also optional - plumed can be used from the compilation directory
\endverbatim
Once the above is completed you can use PLUMED to analyze
@@ -87,7 +87,7 @@ in place so as to do some checking you can use
> ./configure --enable-debug
\endverbatim
This will perform some extra check during execution (possibly slowing down PLUMED)
-and write full symbol tables in the executable (making the final executible much larger).
+and write full symbol tables in the executable (making the final executable much larger).
The main goal of the automatic configure is to find the libraries.
When they are stored in unconventional places it is thus sensible to tell autoconf where
@@ -124,7 +124,8 @@ a specific version of a library by specifying it using the LIBS variable.
if you have problems in linking the file 'src/lib/plumed-shared', try to set correctly
the runtime path by using
\verbatim
-> ./configure LDFLAGS="-L/opt/local/lib -Wl,-rpath,/opt/local/lib" CPPFLAGS=-I/opt/local/include LIBS=-lmymatheval
+> ./configure LDFLAGS="-L/opt/local/lib -Wl,-rpath,/opt/local/lib" \
+ CPPFLAGS=-I/opt/local/include LIBS=-lmymatheval
\endverbatim
Notice that although the file 'src/lib/plumed-shared' is not necessary, being
able to produce it means that it will be possible to link PLUMED dynamically
@@ -193,12 +194,13 @@ Some simple to fix further problems include:
- If the linker complains and suggests recompiling lapack with -fPIC, it means that you have static lapack libraries. Either install dynamic lapack libraries
or switch to static compilation of PLUMED by unsetting the SOEXT variable
in the configuration file.
-- If the linker complains that dsyevr_ cannot be found, try adding
- -DF77_NO_UNDERSCORE to CPPFLAGS
- If the linker complains about other missing functions (typically starting with
"for_" prefix) then you should also link some Fortran libraries. PLUMED
is written in C++ and often C++ linkers do not include Fortran libraries by default.
These libraries are required for lapack and blas to work. Please check the documentation of your compiler.
+- If the linker complains that dsyevr_ cannot be found, try adding
+ -DF77_NO_UNDERSCORE to CPPFLAGS
+ Notice that "./configure" should automatically try this solution.
\section CompilingPlumed Compiling PLUMED
@@ -337,7 +339,10 @@ do not want to set up modules, but we believe that using modules as described ab
\section Patching Patching your MD code
-At the present times PLUMED can be added to the following list of codes:
+In case your MD code is not supporting PLUMED already, you should modify it.
+We provide scripts to adjust some of the most popular MD codes
+so as to provide PLUMED support.
+At the present times we support patching the following list of codes:
@CODESL@
@@ -394,17 +399,18 @@ ALMOST 2.1 can be found in branches/almost-2.1/ and can be compiled:
\warning ALMOST needs SQLITE3, GZIP and BZIP2 installed on your computer.
\verbatim
-./configure --prefix="wherever you want it"
-make
-make install
+> ./configure --prefix="wherever you want it"
+> make
+> make install
\endverbatim
PLUMED will not use the RDCs module of ALMOST so you can ignore the warning about LAPACK.
-Once ALMOST is installeed, PLUMED 2 can then be configured with ALMOST enabled:
+Once ALMOST is installed, PLUMED 2 can then be configured with ALMOST enabled:
\verbatim
-./configure --enable-almost CPPFLAGS="-I/ALMOST_INSTALL_PATH/include -I/ALMOST_INSTALL_PATH/include/almost" LDFLAGS="-L/ALMOST_INSTALL_PATH/lib"
+> ./configure --enable-almost CPPFLAGS="-I/ALMOST_INSTALL_PATH/include \
+ -I/ALMOST_INSTALL_PATH/include/almost" LDFLAGS="-L/ALMOST_INSTALL_PATH/lib"
\endverbatim
with ALMOST_INSTALL_PATH set to the full path to the ALMOST installation folder.
diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt
index 72786b53fb2d0d7c137c578ba3e2516c6deb42b8..f2e78dcc1a2e4374143985904db8d3c4ef1b4de6 100644
--- a/user-doc/Intro.txt
+++ b/user-doc/Intro.txt
@@ -55,12 +55,16 @@ analsyis tools that come with PLUMED are given in:
- \ref Analysis tells you about the various forms of analysis you can run on trajectories using PLUMED.
- \ref Bias tells you about the methods that you can use to bias molecular dynamics simulations with PLUMED.
-PLUMED can be used in one of two ways. It can be incorporated into any one of the MD codes listed below:
+PLUMED can be used in one of two ways.
+First, it can be incorporated into an MD code and used to analyse or bias a molecular dynamics run on the fly.
+Notice that some MD code could already include calls to the PLUMED library
+and be PLUMED-ready in its original distribution (check MD code documentation).
+Additionally, we provide patching procedures for the following codes:
@CODESL@
-and used to analyse or bias a molecular dynamics run on the fly. Alternatively, one
-can use it as a standalone tool for postprocessing the results from molecular dynamics
+Alternatively, one
+can use PLUMED as a standalone tool for postprocessing the results from molecular dynamics
or enhanced sampling calculations.
\page Changelog Change Log
diff --git a/user-doc/Misc.txt b/user-doc/Misc.txt
index 4ff32426fe26be1460cd6435a1fc23b162e3b2c4..5bf6d50de0ba4c03b324b8fc6ab78c2f0ec29724 100644
--- a/user-doc/Misc.txt
+++ b/user-doc/Misc.txt
@@ -21,7 +21,8 @@ erm... yes add lines of comments or trailing comments to your hearts content as
\verbatim
# This is the distance between two atoms:
DISTANCE ATOM=1,2 LABEL=d1
-UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall. That I, one Snout by name, present a wall.
+UPPER_WALLS ARG=d1 AT=3.0 KAPPA=3.0 LABEL=Snout # In this same interlude it doth befall.
+# That I, one Snout by name, present a wall.
\endverbatim
(see \ref DISTANCE and \ref UPPER_WALLS)
diff --git a/user-doc/Syntax.txt b/user-doc/Syntax.txt
index 35adba7733b963146488d8b4dec62c2107fc47a7..2927d5f256be65d7adb078cce6959566fb575ba1 100644
--- a/user-doc/Syntax.txt
+++ b/user-doc/Syntax.txt
@@ -16,7 +16,7 @@ word in these lines specify what particular action is to be performed. This is
which provide PLUMED with more details as to how the action is to be performed. These keywords are either single words
(in which they tell PLUMED to do the calculation in a particular way - for example NOPBC tells PLUMED to not use the periodic
bounadry conditions when calculating a particular colvar) or they can be words followed by an equals sign and a comma separated
-list - WITH NO SPACES - of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in
+list _with no spaces_ of numbers or characters (so for example ATOMS=1,2,3,4 tells PLUMED to use atom numbers 1,2,3 and 4 in
the calculation of a particular colvar). Space separated lists can be used instead of commma separated list if the entire list
is enclosed in curly braces (e.g. ATOMS={1 2 3 4}). Please note that you can split commands over multiple lines by using
\ref ContinuationLines.