diff --git a/CHANGES/v2.4.txt b/CHANGES/v2.4.txt
index 1e476f48969a7f36adc93ae5d5d8ecb9bfc58f74..a7d60ac3d0c0f3567977a8943ff6bef4f3824712 100644
--- a/CHANGES/v2.4.txt
+++ b/CHANGES/v2.4.txt
@@ -29,6 +29,7 @@ Changes from version 2.3 which are relevant for users:
- \ref METAD : BIASFACTOR=1 is allowed and performs unbiased sampling. HILLS file can be used
to recover free energy also in this case.
- Internal molfile implementation has been updated to VMD 1.9.3.
+ - Examples in the documentation now have syntax highlighting and links to the documentation of used actions.
Changes from version 2.3 which are relevant for developers:
- A few fixes has been made to improve exception safety. Although we still cannot declare
diff --git a/README.md b/README.md
index 4a619ac3195ebc6019e52d74b5f310e468808bf0..0ea2a1c5015a338a276d1697446c808bbffff8d5 100644
--- a/README.md
+++ b/README.md
@@ -34,8 +34,8 @@ Below you find the status on [Travis-CI](http://travis-ci.org/plumed/plumed2) fo
|:--------:|:-------------:|:--------:|:------:|
| master | [](https://travis-ci.org/plumed/plumed2) | v2.4 is expected late 2017 | / |
| v2.3 | [](https://travis-ci.org/plumed/plumed2) | Dec 12, 2016 | yes |
-| v2.2 | [](https://travis-ci.org/plumed/plumed2) | Oct 13, 2015 |no |
-| v2.1 | [](https://travis-ci.org/plumed/plumed2) | Sep 9, 2014 | no |
+| v2.2 | [](https://travis-ci.org/plumed/plumed2) | Oct 13, 2015 |no |
+| v2.1 | [](https://travis-ci.org/plumed/plumed2) | Sep 9, 2014 | no |
| v2.0 | Not available | Sep 27, 2013 | no |
Content
diff --git a/src/adjmat/ClusterDiameter.cpp b/src/adjmat/ClusterDiameter.cpp
index ec26f2eeb90e42397f6fca68ed957532a1596581..8bebeab9289b82087748d6ba2ac6969087fe7d69 100644
--- a/src/adjmat/ClusterDiameter.cpp
+++ b/src/adjmat/ClusterDiameter.cpp
@@ -40,7 +40,7 @@ than 2.0 and if they are within 6.0 nm of each other. Depth first search cluste
between every pair of atoms that are within the largest of the clusters found is then calculated and the largest of these distances is output to a file named
colvar.
-\verbatim
+\plumedfile
# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
# Select coordination numbers that are more than 2.0
@@ -52,7 +52,7 @@ dfs: DFSCLUSTERING MATRIX=mat
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1
dia: CLUSTER_DIAMETER CLUSTERS=dfs CLUSTER=1
PRINT ARG=dia FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterDistribution.cpp b/src/adjmat/ClusterDistribution.cpp
index 93f12fb04c16574535bd87bcc34e37bd91daf53c..afd7c956e523eb39e4120713f722c3d9fbf76e5e 100644
--- a/src/adjmat/ClusterDistribution.cpp
+++ b/src/adjmat/ClusterDistribution.cpp
@@ -44,7 +44,7 @@ algorithm on the corresponding graph. The number of componets in this graph that
As discussed in \cite tribello-clustering this input was used to analyse the formation of a polycrystal of GeTe from amorphous
GeTe.
-\verbatim
+\plumedfile
q6: Q6 SPECIES=1-32768 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM
lq6: LOCAL_Q6 SPECIES=q6 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM
flq6: MFILTER_MORE DATA=lq6 SWITCH={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}
@@ -54,7 +54,7 @@ mat: CONTACT_MATRIX ATOMS=fcc SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
dfs: DFSCLUSTERING MATRIX=mat
nclust: CLUSTER_DISTRIBUTION CLUSTERS=dfs TRANSFORM={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0} MORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}
PRINT ARG=nclust.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterProperties.cpp b/src/adjmat/ClusterProperties.cpp
index 9a0d38e5be9d1460ff001f57992e5cd2a9507201..b1d891fe06f55fc5acdfc63ac8fd617d14c13e25 100644
--- a/src/adjmat/ClusterProperties.cpp
+++ b/src/adjmat/ClusterProperties.cpp
@@ -42,13 +42,13 @@ a graph. This dfs action then finds the largest connected component in this gra
numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar
file. The way this input can be used is described in detail in \cite tribello-clustering.
-\verbatim
+\plumedfile
lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45 D_MAX=0.55} LOWMEM
cm: CONTACT_MATRIX ATOMS=lq SWITCH={CUBIC D_0=0.45 D_MAX=0.55}
dfs: DFSCLUSTERING MATRIX=cm
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM
PRINT ARG=clust1.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterSize.cpp b/src/adjmat/ClusterSize.cpp
index b0b22621d6b60a539054a095cf361a5ba0303988..4ae18bb491060052ff566ff3a686c16f9ef0dda4 100644
--- a/src/adjmat/ClusterSize.cpp
+++ b/src/adjmat/ClusterSize.cpp
@@ -39,7 +39,7 @@ The following input uses PLUMED to calculate a adjacency matrix that connects a
than 2.0 and if they are within 6.0 nm of each other. Depth first search clustering is used to find the connected components in this matrix and then
the number of atoms in the largest cluster is found. This quantity is then output to a file called colvar
-\verbatim
+\plumedfile
# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
# Select coordination numbers that are more than 2.0
@@ -51,7 +51,7 @@ dfs: DFSCLUSTERING MATRIX=mat
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1
nat: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1
PRINT ARG=nat FILE=COLVAR
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ClusterWithSurface.cpp b/src/adjmat/ClusterWithSurface.cpp
index ab472eee503791b75715cc02642baa29f6398874..1042accd051e4c0e25008f9df7fa580bc101cbfe 100644
--- a/src/adjmat/ClusterWithSurface.cpp
+++ b/src/adjmat/ClusterWithSurface.cpp
@@ -44,7 +44,7 @@ number of atoms with indices that are between 1 and 1996 and that are either in
atoms within the the second largest cluster are then counted and this number of atoms is output to a file called size. In addition the indices of the atoms
that were counted are output to a file called dfs2.dat.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
@@ -53,7 +53,7 @@ clust2a: CLUSTER_WITHSURFACE CLUSTERS=dfs RCUT_SURF=0.3
size2a: CLUSTER_NATOMS CLUSTERS=clust2a CLUSTER=2
PRINT ARG=size2a FILE=size FMT=%8.4f
OUTPUT_CLUSTER CLUSTERS=clust2a CLUSTER=2 FILE=dfs2.dat
-\endverbatim
+\endplumedfile
*/
diff --git a/src/adjmat/ContactAlignedMatrix.cpp b/src/adjmat/ContactAlignedMatrix.cpp
index e1bdfcdba0a18811235db2b8335482cfed924f32..d00542aea1abc7d94123f9f4ee2c4173bf70adef 100644
--- a/src/adjmat/ContactAlignedMatrix.cpp
+++ b/src/adjmat/ContactAlignedMatrix.cpp
@@ -57,12 +57,12 @@ is greater than 0.5. The sum of the rows of this matrix are then computed. The
many of the molecules that are within the first coordination sphere of molecule \f$i\f$ have an orientation that is similar to that of
molecule \f$i\f$. We thus calculate the number of these "coordination numbers" that are greater than 1.0 and output this quantity to a file.
-\verbatim
+\plumedfile
m1: MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8
mat: ALIGNED_MATRIX ATOMS=m1 SWITCH={RATIONAL R_0=0.1} ORIENTATION_SWITCH={RATIONAL R_0=0.1 D_MAX=0.5}
rr: ROWSUMS MATRIX=mat MORE_THAN={RATIONAL D_0=1.0 R_0=0.1}
PRINT ARG=rr.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/ContactMatrix.cpp b/src/adjmat/ContactMatrix.cpp
index 1105a1aa230d4bf7f9437f8c74eb2cdabbc1d17f..e1a332a2af9a21f8ac2b7f703c27ea450ad9dcfc 100644
--- a/src/adjmat/ContactMatrix.cpp
+++ b/src/adjmat/ContactMatrix.cpp
@@ -48,11 +48,11 @@ The input shown below calculates a \f$6 \times 6\f$ matrix whose elements are eq
of each other and which is zero otherwise. The columns in this matrix are then summed so as to give the coordination number for each atom.
The final quantity output in the colvar file is thus the average coordination number.
-\verbatim
+\plumedfile
aa: CONTACT_MATRIX ATOMS=1-6 SWITCH={EXP D_0=0.2 R_0=0.1 D_MAX=0.66}
COLUMNSUMS MATRIX=mat MEAN LABEL=csums
PRINT ARG=csums.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/DFSClustering.cpp b/src/adjmat/DFSClustering.cpp
index af0dc327e8738a5590f72f12d68bdb404d66c738..23bf5c592caafc058baef4ba28a3bb17303c9ed2 100644
--- a/src/adjmat/DFSClustering.cpp
+++ b/src/adjmat/DFSClustering.cpp
@@ -53,13 +53,13 @@ a graph. This dfs action then finds the largest connected component in this gra
numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar
file. The way this input can be used is described in detail in \cite tribello-clustering.
-\verbatim
+\plumedfile
lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45 D_MAX=0.55} LOWMEM
cm: CONTACT_MATRIX ATOMS=lq SWITCH={CUBIC D_0=0.45 D_MAX=0.55}
dfs: DFSCLUSTERING MATRIX=cm
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM
PRINT ARG=clust1.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/HbondMatrix.cpp b/src/adjmat/HbondMatrix.cpp
index f75e95754bb1697b4b1d474beb11e3f73ad72ba4..32e7989deee60972a4cad90ffe7008730109226f 100644
--- a/src/adjmat/HbondMatrix.cpp
+++ b/src/adjmat/HbondMatrix.cpp
@@ -66,13 +66,13 @@ on the number of hydrogen bonds each of the water molecules donates and accepts.
five columns of data. The first four of these columns are a label for the atom and the x, y and z position of the oxygen. The last column is then
the number of accepted/donated hydrogen bonds.
-\verbatim
+\plumedfile
mat: HBOND_MATRIX ATOMS=1-192:3 HYDROGENS=2-192:3,3-192:3 SWITCH={RATIONAL R_0=3.20} HSWITCH={RATIONAL R_0=2.30} ASWITCH={RATIONAL R_0=0.167pi} SUM
rsums: ROWSUMS MATRIX=mat MEAN
csums: COLUMNSUMS MATRIX=mat MEAN
DUMPMULTICOLVAR DATA=rsums FILE=donors.xyz
DUMPMULTICOLVAR DATA=csums FILE=acceptors.x
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/MatrixColumnSums.cpp b/src/adjmat/MatrixColumnSums.cpp
index 7735023490ce6b93abc91d88cc1cfb47f75fd048..cae24fcec899d62d88cc879ead801480d41a35a5 100644
--- a/src/adjmat/MatrixColumnSums.cpp
+++ b/src/adjmat/MatrixColumnSums.cpp
@@ -43,21 +43,21 @@ tells you whether atoms \f$i\f$ and \f$j\f$ are within 1.0 nm of each other. Th
and the average value is computed. As such the following input provides an alternative method for calculating the coordination numbers
of atoms 1 to 10.
-\verbatim
+\plumedfile
mat: CONTACT_MATRIX ATOMS=1-10 SWITCH={RATIONAL R_0=1.0}
rsums: COLUMNSUMS MATRIX=mat MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
The following input demonstrates another way that an average coordination number can be computed. This input calculates the number of atoms
with indices between 1 and 5 that are within the first coordination spheres of each of the atoms within indices between 6 and 15. The average
coordination number is then calculated from these fifteen coordination numbers and this quantity is output to a file.
-\verbatim
+\plumedfile
mat2: CONTACT_MATRIX ATOMSA=1-5 ATOMSB=6-15 SWITCH={RATIONAL R_0=1.0}
rsums: COLUMNSUMS MATRIX=mat2 MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/MatrixRowSums.cpp b/src/adjmat/MatrixRowSums.cpp
index 038aa89a71fe36d25487433f621811ec705c3200..6ef15fb282c0ddabd29136e1a6ed55ba668e1cfd 100644
--- a/src/adjmat/MatrixRowSums.cpp
+++ b/src/adjmat/MatrixRowSums.cpp
@@ -43,21 +43,21 @@ tells you whether atoms \f$i\f$ and \f$j\f$ are within 1.0 nm of each other. Th
and the average value is computed. As such the following input provides an alternative method for calculating the coordination numbers
of atoms 1 to 10.
-\verbatim
+\plumedfile
mat: CONTACT_MATRIX ATOMS=1-10 SWITCH={RATIONAL R_0=1.0}
rsums: ROWSUMS MATRIX=mat MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
The following input demonstrates another way that an average coordination number can be computed. This input calculates the number of atoms
with indices between 6 and 15 that are within the first coordination spheres of each of the atoms within indices between 1 and 5. The average
coordination number is then calculated from these five coordination numbers and this quantity is output to a file.
-\verbatim
+\plumedfile
mat2: CONTACT_MATRIX ATOMSA=1-5 ATOMSB=6-15 SWITCH={RATIONAL R_0=1.0}
rsums: ROWSUMS MATRIX=mat2 MEAN
PRINT ARG=rsums.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/OutputCluster.cpp b/src/adjmat/OutputCluster.cpp
index c2b752f0d0821c70254e7da7e90f57588649f0cb..4dd430f3c71befba4c75b6a443e61b1698ab1ddc 100644
--- a/src/adjmat/OutputCluster.cpp
+++ b/src/adjmat/OutputCluster.cpp
@@ -47,13 +47,13 @@ that satisfy this criteria. The DFS algorithm is then used to find the connecte
in this matrix and the indices of the atoms in the largest connected component are then output
to a file.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
dfs: DFSCLUSTERING MATRIX=mat
OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=dfs.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/SMACMatrix.cpp b/src/adjmat/SMACMatrix.cpp
index ac433076bd9abef860031586015ac4810af0869b..a4e8288f49f5e12b0dfd07db3bb77eaeb1fe8882 100644
--- a/src/adjmat/SMACMatrix.cpp
+++ b/src/adjmat/SMACMatrix.cpp
@@ -49,7 +49,7 @@ molecules \f$i\f$ and \f$j\f$ are within 6 angstroms of each other and if the to
of these molecules is close to 0 or \f$\pi\f$. The various connected components of this matrix are determined using the
\ref DFSCLUSTERING algorithm and then the size of the largest cluster of connectes molecules is output to a colvar file
-\verbatim
+\plumedfile
UNITS LENGTH=A
MOLECULES ...
@@ -70,7 +70,7 @@ SMAC_MATRIX ...
dfs1: DFSCLUSTERING MATRIX=smacm
cc2: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1
PRINT ARG=smac.*,cc1.*,cc2 FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/adjmat/Sprint.cpp b/src/adjmat/Sprint.cpp
index f7e0a0da8f5ff58c6fe3b2950c4e3156f6ac726e..3e90100e8e2d6c139b559a220e0edcb3d04e996e 100644
--- a/src/adjmat/Sprint.cpp
+++ b/src/adjmat/Sprint.cpp
@@ -46,17 +46,17 @@ This example input calculates the 7 SPRINT coordinates for a 7 atom cluster of L
atoms and prints their values to a file. In this input the SPRINT coordinates are calculated
in the manner described in ?? so two atoms are adjacent if they are within a cutoff:
-\verbatim
+\plumedfile
DENSITY SPECIES=1-7 LABEL=d1
CONTACT_MATRIX ATOMS=d1 SWITCH={RATIONAL R_0=0.1} LABEL=mat
SPRINT MATRIX=mat LABEL=ss
PRINT ARG=ss.* FILE=colvar
-\endverbatim
+\endplumedfile
This example input calculates the 14 SPRINT coordinates foa a molecule composed of 7 hydrogen and
7 carbon atoms. Once again two atoms are adjacent if they are within a cutoff:
-\verbatim
+\plumedfile
DENSITY SPECIES=1-7 LABEL=c
DENSITY SPECIES=8-14 LABEL=h
@@ -71,7 +71,7 @@ CONTACT_MATRIX ...
SPRINT MATRIX=mat LABEL=ss
PRINT ARG=ss.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/Average.cpp b/src/analysis/Average.cpp
index c96b2556bbe11df0fd4ae0b4dcd7ac080918d8ca..9d0566da8e2a35c13cecdf769dfabab45e009741 100644
--- a/src/analysis/Average.cpp
+++ b/src/analysis/Average.cpp
@@ -51,11 +51,11 @@ and output this to a file called COLVAR. In this example it is assumed that no
on the system and that the weights, \f$w(t')\f$ in the formulae above can thus all be set equal
to one.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d1a: AVERAGE ARG=d1
PRINT ARG=d1a FILE=colvar STRIDE=100
-\endverbatim
+\endplumedfile
The following example calculates the ensemble average for the torsional angle involving atoms 1, 2, 3 and 4.
At variance with the previous example this quantity is periodic so the second formula in the above introduction
@@ -65,23 +65,23 @@ forgotten and the process of averaging is begun again. The quantities output in
block averages taken over the first 100 frames of the trajectory, the block average over the second 100 frames
of trajectory and so on.
-\verbatim
+\plumedfile
t1: TORSION ATOMS=1,2,3,4
t1a: AVERAGE ARG=t1 CLEAR=100
PRINT ARG=t1a FILE=colvar STRIDE=100
-\endverbatim
+\endplumedfile
This third example incorporates a bias. Notice that the effect the bias has on the ensemble average is removed by taking
advantage of the \ref REWEIGHT_BIAS method. The final ensemble averages output to the file are thus block ensemble averages for the
unbiased canononical ensemble at a temperature of 300 K.
-\verbatim
+\plumedfile
t1: TORSION ATOMS=1,2,3,4
RESTRAINT ARG=t1 AT=pi KAPPA=100.
ww: REWEIGHT_BIAS TEMP=300
t1a: AVERAGE ARG=t1 LOGWEIGHTS=ww CLEAR=100
PRINT ARG=t1a FILE=colvar STRIDE=100
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/ClassicalMultiDimensionalScaling.cpp b/src/analysis/ClassicalMultiDimensionalScaling.cpp
index 93bb25f1d485c7a82d1cbac211952c8678801e23..68ac6aeae304c4b06b38f5878d816ce4100fe3bf 100644
--- a/src/analysis/ClassicalMultiDimensionalScaling.cpp
+++ b/src/analysis/ClassicalMultiDimensionalScaling.cpp
@@ -55,7 +55,7 @@ can be found in the tutorial \ref belfast-3 and in the following <a href="https:
The following command instructs plumed to construct a classical multidimensional scaling projection of a trajectory.
The RMSD distance between atoms 1-256 have moved is used to measure the distances in the high-dimensional space.
-\verbatim
+\plumedfile
CLASSICAL_MDS ...
ATOMS=1-256
METRIC=OPTIMAL-FAST
@@ -63,7 +63,7 @@ CLASSICAL_MDS ...
NLOW_DIM=2
OUTPUT_FILE=rmsd-embed
... CLASSICAL_MDS
-\endverbatim
+\endplumedfile
The following section is for people who are interested in how this method works in detail. A solid understanding of this material is
not necessary to use MDS.
diff --git a/src/analysis/Commit.cpp b/src/analysis/Commit.cpp
index 5cbacf4db1d10ef29c3d5ea8f2c45b612eaab869..d51d6b9e55f12af1600b6da880657438f589c341 100644
--- a/src/analysis/Commit.cpp
+++ b/src/analysis/Commit.cpp
@@ -37,7 +37,7 @@ The following input monitors two torsional angles during a simulation,
defines two basins (A and B) as a function of the two torsions and
stops the simulation when it falls in one of the two. In the log
file will be shown the latest values for the CVs and the basin reached.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
COMMITTOR ...
@@ -48,7 +48,7 @@ COMMITTOR ...
BASIN_LL2=-0.15,-0.20
BASIN_UL2=-0.25,-0.40
... COMMITTOR
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index b8a74c797d8197d4278653f5b77e76f562bc818d..16abb4a6dcb9ffa1791edd7a7721c8ca6dda1d3b 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -84,7 +84,7 @@ Additional material and examples can be also found in the tutorial \ref belfast-
The following input monitors two torsional angles during a simulation
and outputs a continuos histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -97,11 +97,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a discrete histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -115,11 +115,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs the histogram accumulated thus far every 100000 steps.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -132,14 +132,14 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a separate histogram for each 100000 steps worth of trajectory.
Notice how the CLEAR keyword is used here and how it is not used in the
previous example.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -153,7 +153,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/analysis/PCA.cpp b/src/analysis/PCA.cpp
index 5b31a04faafd648f6280c5c1dc173e136dcfc82f..528c6290b73b8648e87d0e73a852db58e2a400eb 100644
--- a/src/analysis/PCA.cpp
+++ b/src/analysis/PCA.cpp
@@ -63,9 +63,9 @@ of the first 22 atoms. The TYPE=OPTIMAL instruction ensures that translational
The first two principal components will be output to a file called pca-comp.pdb. Trajectory frames will be collected on every step and the PCA calculation
will be performed at the end of the simulation.
-\verbatim
+\plumedfile
PCA METRIC=OPTIMAL ATOMS=1-22 STRIDE=1 USE_ALL_DATA NLOW_DIM=2 OFILE=pca-comp.pdb
-\endverbatim
+\endplumedfile
The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from chnages in the six distances
seen in the previous lines. Notice that here the TYPE=EUCLIDEAN keyword is used to indicate that no alighment has to be done when calculating the various
@@ -75,7 +75,7 @@ PCA analysis will be performed twice. The REWEIGHT_BIAS keyword in this input t
when calculating averages and covariances a reweighting should be performed based and each frames' weight in these calculations should be determined based on
the current value of the instantaneous bias (see \ref REWEIGHT_BIAS).
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=1,3
d3: DISTANCE ATOMS=1,4
@@ -84,7 +84,7 @@ d5: DISTANCE ATOMS=2,4
d6: DISTANCE ATOMS=3,4
PCA ARG=d1,d2,d3,d4,d5,d6 METRIC=EUCLIDEAN STRIDE=5 RUN=1000 NLOW_DIM=2 REWEIGHT_BIAS OFILE=pca-comp.pdb
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/ABMD.cpp b/src/bias/ABMD.cpp
index 5e8bef344e96a30c09e23d149f31709a06e9bc62..a76c5341c3b983cde34534ea31f8c57d18949113 100644
--- a/src/bias/ABMD.cpp
+++ b/src/bias/ABMD.cpp
@@ -70,13 +70,12 @@ an additional white noise acting on the minimum position of the bias.
The following input sets up two biases, one on the distance between atoms 3 and 5
and another on the distance between atoms 2 and 4. The two target values are defined
using TO and the two strength using KAPPA. The total energy of the bias is printed.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
ABMD ARG=d1,d2 TO=1.0,1.5 KAPPA=5.0,5.0 LABEL=abmd
PRINT ARG=abmd.bias,abmd.d1_min,abmd.d2_min
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/BiasValue.cpp b/src/bias/BiasValue.cpp
index 3e77621a55546b1510f126fbdd20e40f935efbfa..ff741a6c0c5c3e0e7b9b265fe11664d6442a7d10 100644
--- a/src/bias/BiasValue.cpp
+++ b/src/bias/BiasValue.cpp
@@ -42,18 +42,17 @@ to some collective variable then using the value of this function directly as a
The following input tells plumed to use the value of the distance between atoms 3 and 5
and the value of the distance between atoms 2 and 4 as biases.
It then tells plumed to print the energy of the restraint
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=3,6 LABEL=d2
BIASVALUE ARG=d1,d2 LABEL=b
PRINT ARG=d1,d2,b.d1,b.d2
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
Another thing one can do is asking one system to follow
a circle in sin/cos according a time dependence
-\verbatim
+\plumedfile
t: TIME
# this just print cos and sin of time
cos: MATHEVAL ARG=t VAR=t FUNC=cos(t) PERIODIC=NO
@@ -72,9 +71,7 @@ vv1: MATHEVAL ARG=mycos,mysin,cos,sin VAR=mc,ms,c,s FUNC=100*((mc-c)^2+(ms-s)^
cc: BIASVALUE ARG=vv1
# some printout
PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.bias.vv1 STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
-(see also \ref TIME, \ref MATHEVAL, \ref COM, \ref DISTANCE, and \ref PRINT).
-
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/ExtendedLagrangian.cpp b/src/bias/ExtendedLagrangian.cpp
index 85de570dd5030e1c58e3a513d7747e7da5a2e2ed..ee3d3ada041452f28b612d2295b363c18ec80eca 100644
--- a/src/bias/ExtendedLagrangian.cpp
+++ b/src/bias/ExtendedLagrangian.cpp
@@ -88,28 +88,26 @@ and many shorter runs.
The following input tells plumed to perform a metadynamics
with an extended Lagrangian on two torsional angles.
-\verbatim
+\plumedfile
phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17
ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1
METAD ARG=ex.phi_fict,ex.psi_fict PACE=100 SIGMA=0.35,0.35 HEIGHT=0.1
# monitor the two variables
PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR
-\endverbatim
-(See also \ref TORSION, \ref METAD, and \ref PRINT).
+\endplumedfile
The following input tells plumed to perform a TAMD (or dAFED)
calculation on two torsional angles, keeping the two variables
at a fictitious temperature of 3000K with a Langevin thermostat
with friction 10
-\verbatim
+\plumedfile
phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17
ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1 FRICTION=10,10 TEMP=3000
# monitor the two variables
PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR
-\endverbatim
-(See also \ref TORSION and \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 62bc54cf9252fc9102014483546b697d5b765816..7c714efae64d1c6568d29efa0e70b36fd7721353 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -39,11 +39,10 @@ Calculate a restraint that is defined on a grid that is read during start up
\par Examples
The following is an input for a calculation with an external potential that is
defined in the file bias.dat and that acts on the distance between atoms 3 and 5.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
EXTERNAL ARG=d1 FILE=bias.dat LABEL=external
-\endverbatim
-(See also \ref DISTANCE \ref PRINT).
+\endplumedfile
The header in the file bias.dat should read:
\verbatim
@@ -61,11 +60,11 @@ with NOSPLINE you do not need to provide derivative information.
You can also include grids that are a function of more than one collective
variable. For instance the following would be the input for an external
potential acting on two torsional angles:
-\verbatim
+\plumedfile
TORSION ATOMS=4,5,6,7 LABEL=t1
TORSION ATOMS=6,7,8,9 LABEL=t2
EXTERNAL ARG=t1,t2 FILE=bias.dat LABEL=ext
-\endverbatim
+\endplumedfile
The header in the file bias.dat for this calculation would read:
\verbatim
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index 33d7f7c04604a5a0217e918f4c200ff5b81e0d4b..26bb720f13ba11b7417230db587402eb8bc17e26 100644
--- a/src/bias/LWalls.cpp
+++ b/src/bias/LWalls.cpp
@@ -52,13 +52,13 @@ The following input tells plumed to add both a lower and an upper walls on the d
between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
are defined at different values. The strength of the walls is the same for the four cases.
It also tells plumed to print the energy of the walls.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall
LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall
PRINT ARG=uwall.bias,lwall.bias
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE and \ref PRINT).
*/
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index b586185705abc526b20c18ce567923982896535f..5023c38f2cfec80681d7ad36bb731d1b96607e6b 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -163,35 +163,35 @@ The following input is for a standard metadynamics calculation using as
collective variables the distance between atoms 3 and 5
and the distance between atoms 2 and 4. The value of the CVs and
the metadynamics bias potential are written to the COLVAR file every 100 steps.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3 PACE=500 LABEL=restraint
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE \ref PRINT).
\par
If you use adaptive Gaussians, with diffusion scheme where you use
a Gaussian that should cover the space of 20 timesteps in collective variables.
Note that in this case the histogram correction is needed when summing up hills.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ARG=d1,d2 SIGMA=20 HEIGHT=0.3 PACE=500 LABEL=restraint ADAPTIVE=DIFF
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
If you use adaptive Gaussians, with geometrical scheme where you use
a Gaussian that should cover the space of 0.05 nm in Cartesian space.
Note that in this case the histogram correction is needed when summing up hills.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ARG=d1,d2 SIGMA=0.05 HEIGHT=0.3 PACE=500 LABEL=restraint ADAPTIVE=GEOM
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
When using adaptive Gaussians you might want to limit how the hills width can change.
@@ -199,7 +199,7 @@ You can use SIGMA_MIN and SIGMA_MAX keywords.
The sigmas should specified in terms of CV so you should use the CV units.
Note that if you use a negative number, this means that the limit is not set.
Note also that in this case the histogram correction is needed when summing up hills.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
METAD ...
@@ -207,7 +207,7 @@ METAD ...
SIGMA_MIN=0.2,0.1 SIGMA_MAX=0.5,1.0
... METAD
PRINT ARG=d1,d2,restraint.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
Multiple walkers can be also use as in \cite multiplewalkers
@@ -215,7 +215,7 @@ These are enabled by setting the number of walker used, the id of the
current walker which interprets the input file, the directory where the
hills containing files resides, and the frequency to read the other walkers.
Here is an example
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
METAD ...
ARG=d1 SIGMA=0.05 HEIGHT=0.3 PACE=500 LABEL=restraint
@@ -224,7 +224,7 @@ METAD ...
WALKERS_DIR=../
WALKERS_RSTRIDE=100
... METAD
-\endverbatim
+\endplumedfile
where WALKERS_N is the total number of walkers, WALKERS_ID is the
id of the present walker (starting from 0 ) and the WALKERS_DIR is the directory
where all the walkers are located. WALKERS_RSTRIDE is the number of step between
@@ -237,7 +237,7 @@ presented in \cite Tiwary_jp504920s as described above.
This is enabled by using the keyword REWEIGHTING_NGRID where the grid used for
the calculation is set. The number of grid points given in REWEIGHTING_NGRID
should be equal or larger than the number of grid points given in GRID_BIN.
-\verbatim
+\plumedfile
METAD ...
LABEL=metad
ARG=phi,psi SIGMA=0.20,0.20 HEIGHT=1.20 BIASFACTOR=5 TEMP=300.0 PACE=500
@@ -245,7 +245,7 @@ METAD ...
REWEIGHTING_NGRID=150,150
REWEIGHTING_NHILLS=20
... METAD
-\endverbatim
+\endplumedfile
Here we have asked that the calculation is performed every 20 hills by using
REWEIGHTING_NHILLS keyword. If this keyword is not given the calculation will
by default be performed every 50 hills. The c(t) reweighting factor will be given
@@ -285,7 +285,7 @@ Alternatively, if you use a BIASFACTOR yout simulation will converge to a free
energy that is a linear combination of the target free energy and of the intrinsic free energy
determined by the original force field.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
METAD ...
LABEL=t1
@@ -295,7 +295,7 @@ METAD ...
... METAD
PRINT ARG=d1,t1.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
The header in the file dist.dat for this calculation would read:
@@ -309,19 +309,19 @@ The header in the file dist.dat for this calculation would read:
Notice that BIASFACTOR can also be chosen as equal to 1. In this case one will perform
unbiased sampling. Instead of using HEIGHT, one should provide the TAU parameter.
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=3,5
METAD ARG=d SIGMA=0.1 TAU=4.0 TEMP=300 PACE=100 BIASFACTOR=1.0
-\endverbatim
+\endplumedfile
The HILLS file obtained will still work with `plumed sum_hills` so as to plot a free-energy.
The case where this makes sense is probably that of RECT simulations.
Regarding RECT simulations, you can also use the RECT keyword so as to avoid using multiple input files.
For instance, a single input file will be
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=3,5
METAD ARG=d SIGMA=0.1 TAU=4.0 TEMP=300 PACE=100 RECT=1.0,1.5,2.0,3.0
-\endverbatim
+\endplumedfile
The number of elements in the RECT array should be equal to the number of replicas.
diff --git a/src/bias/Metainference.cpp b/src/bias/Metainference.cpp
index e4d3e8b94f0d63194082568859b63d1beafc5dd4..3953c436d1368922505817caa483ff033bc6ccb2 100644
--- a/src/bias/Metainference.cpp
+++ b/src/bias/Metainference.cpp
@@ -58,7 +58,7 @@ them and comparing them with a set of experimental values. RDCs are compared wit
the experimental data but for a multiplication factor SCALE that is also sampled by
MC on-the-fly
-\verbatim
+\plumedfile
RDC ...
LABEL=rdc
SCALE=0.0001
@@ -83,12 +83,12 @@ LABEL=spe
... METAINFERENCE
PRINT ARG=spe.bias FILE=BIAS STRIDE=1
-\endverbatim
+\endplumedfile
in the following example instead of using one uncertainty parameter per data point we use
a single uncertainty value in a long-tailed gaussian to take into account for outliers.
-\verbatim
+\plumedfile
METAINFERENCE ...
ARG=ardc.*
NOISETYPE=OUTLIERS
@@ -99,9 +99,7 @@ SIGMA_MEAN=0.001
TEMP=300
LABEL=spe
... METAINFERENCE
-\endverbatim
-
-(See also \ref RDC and \ref ENSEMBLE).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index 13cafce97e63a71aa0a76718229986d4095963b4..d5317af1d9abb8a0e4e0771eede4b68e49e3681e 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -53,7 +53,7 @@ Additional material and examples can be also found in the tutorial \ref belfast-
The following input is dragging the distance between atoms 2 and 4
from 1 to 2 in the first 1000 steps, then back in the next 1000 steps.
In the following 500 steps the restraint is progressively switched off.
-\verbatim
+\plumedfile
DISTANCE ATOMS=2,4 LABEL=d
MOVINGRESTRAINT ...
ARG=d
@@ -62,12 +62,12 @@ MOVINGRESTRAINT ...
STEP2=2000 AT2=1.0
STEP3=2500 KAPPA3=0.0
... MOVINGRESTRAINT
-\endverbatim
+\endplumedfile
The following input is progressively building restraints
distances between atoms 1 and 5 and between atoms 2 and 4
in the first 1000 steps. Afterwards, the restraint is kept
static.
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
MOVINGRESTRAINT ...
@@ -75,10 +75,10 @@ MOVINGRESTRAINT ...
STEP0=0 AT0=1.0,1.5 KAPPA0=0.0,0.0
STEP1=1000 AT1=1.0,1.5 KAPPA1=1.0,1.0
... MOVINGRESTRAINT
-\endverbatim
+\endplumedfile
The following input is progressively bringing atoms 1 and 2
close to each other with an upper wall
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,2 LABEL=d1
MOVINGRESTRAINT ...
ARG=d1
@@ -86,7 +86,7 @@ MOVINGRESTRAINT ...
STEP0=0 AT0=1.0 KAPPA0=10.0
STEP1=1000 AT1=0.0
... MOVINGRESTRAINT
-\endverbatim
+\endplumedfile
By default the Action is issuing some values which are
the work on each degree of freedom, the center of the harmonic potential,
diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
index b50557f7d297f59f61da770a9ce711a77415f9ed..76c35154bd6b648132fb5396ca88fec4f694edea 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -150,18 +150,18 @@ The following input is for PBMetaD calculation using as
collective variables the distance between atoms 3 and 5
and the distance between atoms 2 and 4. The value of the CVs and
the PBMetaD bias potential are written to the COLVAR file every 100 steps.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3 PACE=500 LABEL=pb FILE=HILLS_d1,HILLS_d2
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE and \ref PRINT).
\par
If you use well-tempered metadynamics, you should specify a single biasfactor and initial
Gaussian height.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ...
@@ -170,11 +170,11 @@ PACE=500 BIASFACTOR=8 LABEL=pb
FILE=HILLS_d1,HILLS_d2
... PBMETAD
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
The following input enables the MPI version of multiple-walkers.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ...
@@ -184,7 +184,7 @@ FILE=HILLS_d1,HILLS_d2
WALKERS_MPI
... PBMETAD
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
\par
The disk version of multiple-walkers can be
@@ -192,7 +192,7 @@ enabled by setting the number of walker used, the id of the
current walker which interprets the input file, the directory where the
hills containing files resides, and the frequency to read the other walkers.
Here is an example
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
PBMETAD ...
@@ -205,7 +205,7 @@ WALKERS_DIR=../
WALKERS_RSTRIDE=100
... PBMETAD
PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
where WALKERS_N is the total number of walkers, WALKERS_ID is the
id of the present walker (starting from 0 ) and the WALKERS_DIR is the directory
where all the walkers are located. WALKERS_RSTRIDE is the number of step between
diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
index 8bb3df2027989545444b3157fceaf50333034ca0..85208d35ba1ad62377bcbf09bc662fb088261f1e 100644
--- a/src/bias/Restraint.cpp
+++ b/src/bias/Restraint.cpp
@@ -49,13 +49,12 @@ Additional material and examples can be also found in the tutorial \ref belfast-
The following input tells plumed to restrain the distance between atoms 3 and 5
and the distance between atoms 2 and 4, at different equilibrium
values, and to print the energy of the restraint
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
RESTRAINT ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 LABEL=restraint
PRINT ARG=restraint.bias
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/ReweightBias.cpp b/src/bias/ReweightBias.cpp
index d0b2d90a3e64af196838222f2656d920858fc278..60976e644d9d47bd2e931b9faddeaf68568eb049 100644
--- a/src/bias/ReweightBias.cpp
+++ b/src/bias/ReweightBias.cpp
@@ -43,7 +43,7 @@ restraint will have an effect on the region of phase space that will be sampled
run using this variable. Consequently, when the histogram as a function of the distance, \f$x\f$, is accumulated,
we use reweighting into order to discount the effect of the bias from our final histogram.
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
RESTRAINT ARG=x SLOPE=1.0 AT=0.0
as: REWEIGHT_BIAS TEMP=300
@@ -59,7 +59,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hB FILE=histoB STRIDE=1 FMT=%8.4f
-\endverbatim
+\endplumedfile
*/
diff --git a/src/bias/ReweightMetad.cpp b/src/bias/ReweightMetad.cpp
index 766ed40dfcd7b604dff26289fdf25bde58011875..42a4855c24d81e1b51232056c9682c836a05193b 100644
--- a/src/bias/ReweightMetad.cpp
+++ b/src/bias/ReweightMetad.cpp
@@ -39,7 +39,7 @@ we use reweighting into order to discount the effect of the bias from our final
metadynamics instead. Notice also that we have to specify how often we would like to calculate the c(t) reweighting
factor and the grid over which we calculate c(t) in the input to the METAD command.
-\verbatim
+\plumedfile
a: ANGLE ATOMS=1,2,3
x: DISTANCE ATOMS=1,2
METAD ARG=x PACE=100 SIGMA=0.1 HEIGHT=1.5 BIASFACTOR=5 GRID_MIN=0 GRID_MAX=10 GRID_BIN=100 REWEIGHTING_NGRID=100 REWEIGHTING_NHILLS=50
@@ -57,8 +57,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hB FILE=histoB STRIDE=1 FMT=%8.4f
-
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
index 0f096f11b1c8fa109252118ab5241c90a04ded4b..bfe4d8929ef2f3ae245594d70450a80517861f16 100644
--- a/src/bias/UWalls.cpp
+++ b/src/bias/UWalls.cpp
@@ -52,14 +52,13 @@ The following input tells plumed to add both a lower and an upper walls on the d
between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
are defined at different values. The strength of the walls is the same for the four cases.
It also tells plumed to print the energy of the walls.
-\verbatim
+\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
DISTANCE ATOMS=2,4 LABEL=d2
UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall
LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall
PRINT ARG=uwall.bias,lwall.bias
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Angle.cpp b/src/colvar/Angle.cpp
index ed57d03ea56966effc65d70d6153d2a9d56f820e..285d6fa5050eca25969e490cbc96ab4199d34f2b 100644
--- a/src/colvar/Angle.cpp
+++ b/src/colvar/Angle.cpp
@@ -67,7 +67,7 @@ This command tells plumed to calculate the angle between the vector connecting a
the vector connecting atom 2 to atom 3 and to print it on file COLVAR1. At the same time,
the angle between vector connecting atom 1 to atom 2 and the vector connecting atom 3 to atom 4 is printed
on file COLVAR2.
-\verbatim
+\plumedfile
a: ANGLE ATOMS=1,2,3
# equivalently one could state:
@@ -77,8 +77,7 @@ b: ANGLE ATOMS=1,2,3,4
PRINT ARG=a FILE=COLVAR1
PRINT ARG=b FILE=COLVAR2
-\endverbatim
-(see also \ref PRINT)
+\endplumedfile
*/
diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp
index 040e0dfad8c6fdfff0da8c51a9254812f8dcceba..6c606e4e5caef102592328cb1fae021f21afff09 100644
--- a/src/colvar/CS2Backbone.cpp
+++ b/src/colvar/CS2Backbone.cpp
@@ -116,17 +116,17 @@ Additional material and examples can be also found in the tutorial \ref belfast-
In this first example the chemical shifts are used to calculate a scoring function to be used
in NMR driven Metadynamics \cite Granata:2013dk :
-\verbatim
+\plumedfile
whole: GROUP ATOMS=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1
WHOLEMOLECULES ENTITY0=whole
cs: CS2BACKBONE ATOMS=1-2612 NRES=176 DATA=../data/ TEMPLATE=template.pdb CAMSHIFT NOPBC
metad: METAD ARG=cs HEIGHT=0.5 SIGMA=0.1 PACE=200 BIASFACTOR=10
PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100
-\endverbatim
+\endplumedfile
In this second example the chemical shifts are used as replica-averaged restrained as in \cite Camilloni:2012je \cite Camilloni:2013hs.
-\verbatim
+\plumedfile
cs: CS2BACKBONE ATOMS=1-174 DATA=data/ NRES=13
encs: ENSEMBLE ARG=(cs\.hn_.*),(cs\.nh_.*)
stcs: STATS ARG=encs.* SQDEVSUM PARARG=(cs\.exphn_.*),(cs\.expnh_.*)
@@ -134,7 +134,7 @@ RESTRAINT ARG=stcs.sqdevsum AT=0 KAPPA=0 SLOPE=24
PRINT ARG=(cs\.hn_.*),(cs\.nh_.*) FILE=RESTRAINT STRIDE=100
-\endverbatim
+\endplumedfile
(See also \ref WHOLEMOLECULES, \ref STATS, \ref METAD, \ref RESTRAINT and \ref PRINT)
diff --git a/src/colvar/Cell.cpp b/src/colvar/Cell.cpp
index 5c59e9f49dbeae2521e1fb62204edd69617dc599..082fa237dbdba39aceb57dd087ef86f2ee71e370 100644
--- a/src/colvar/Cell.cpp
+++ b/src/colvar/Cell.cpp
@@ -36,14 +36,13 @@ Calculate the components of the simulation cell
\par Examples
The following input tells plumed to print the squared modulo of each of the three lattice vectors
-\verbatim
+\plumedfile
cell: CELL
aaa: COMBINE ARG=cell.ax,cell.ay,cell.az POWERS=2,2,2 PERIODIC=NO
bbb: COMBINE ARG=cell.bx,cell.by,cell.bz POWERS=2,2,2 PERIODIC=NO
ccc: COMBINE ARG=cell.cx,cell.cy,cell.cz POWERS=2,2,2 PERIODIC=NO
PRINT ARG=aaa,bbb,ccc
-\endverbatim
-(See also \ref COMBINE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Constant.cpp b/src/colvar/Constant.cpp
index 49423413dfe307cd33c56cc063c8fd4a3f422e5d..247f9ac6d4ab5366692ac0b4eddada801d7c0691 100644
--- a/src/colvar/Constant.cpp
+++ b/src/colvar/Constant.cpp
@@ -44,21 +44,20 @@ The following input instructs plumed to compute the distance
between atoms 1 and 2. If this distance is between 1.0 and 2.0, it is
printed. If it is lower than 1.0 (larger than 2.0), 1.0 (2.0) is printed
-\verbatim
+\plumedfile
cn: CONSTANT VALUES=1.0,2.0
dis: DISTANCE ATOMS=1,2
sss: SORT ARG=cn.v_0,dis,cn.v_1
PRINT ARG=sss.2
-\endverbatim
-(See also \ref DISTANCE, \ref SORT, and \ref PRINT).
+\endplumedfile
In case you want to pass a single value you can use VALUE:
-\verbatim
+\plumedfile
cn: CONSTANT VALUE=1.0
dis: DISTANCE ATOMS=1
sss: SORT ARG=cn,dis
PRINT ARG=sss.1
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/ContactMap.cpp b/src/colvar/ContactMap.cpp
index 9405f172f4fef5820e3c4bfb7389ba3cec06069a..9fe8f82c9289d32026da05cc7103d69da5e56d17 100644
--- a/src/colvar/ContactMap.cpp
+++ b/src/colvar/ContactMap.cpp
@@ -45,17 +45,17 @@ The following example calculates switching functions based on the distances betw
1 and 2, 3 and 4 and 4 and 5. The values of these three switching functions are then output
to a file named colvar.
-\verbatim
+\plumedfile
CONTACTMAP ATOMS1=1,2 ATOMS2=3,4 ATOMS3=4,5 ATOMS4=5,6 SWITCH={RATIONAL R_0=1.5} LABEL=f1
PRINT ARG=f1.* FILE=colvar
-\endverbatim
+\endplumedfile
The following example calculates the difference of the current contact map with respect
to a reference provided. In this case REFERENCE is the fraction of contact that is formed
(i.e. the distance between two atoms transformed with the SWITH), while R_0 is the contact
distance. WEIGHT gives the relative weight of each contact to the final distance measure.
-\verbatim
+\plumedfile
CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=0.1 WEIGHT1=0.5
ATOMS2=3,4 REFERENCE2=0.5 WEIGHT2=1.0
@@ -67,7 +67,7 @@ CMDIST
... CONTACTMAP
PRINT ARG=cmap FILE=colvar
-\endverbatim
+\endplumedfile
The next example calculates calculates fraction of native contacts (Q)
for Trp-cage mini-protein. R_0 is the distance at which the switch function is guaranteed to
@@ -80,7 +80,7 @@ WEIGHT is the 1/(number of contacts) giving equal weight to each contact.
When using native contact Q switch function, please cite \cite best2013
-\verbatim
+\plumedfile
# Full example available in regtest/basic/rt72/
CONTACTMAP ...
@@ -97,9 +97,8 @@ SUM
... CONTACTMAP
PRINT ARG=cmap FILE=colvar
-\endverbatim
-
-(See also \ref PRINT and \ref switchingfunction)
+\endplumedfile
+(See also \ref switchingfunction)
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Coordination.cpp b/src/colvar/Coordination.cpp
index c1aa2da4f28f631d614b31615432f7c6c2d65871..cf964555895c5fd8fa65e6fa9790c4971ed0968f 100644
--- a/src/colvar/Coordination.cpp
+++ b/src/colvar/Coordination.cpp
@@ -62,28 +62,34 @@ so that they actually count as "zero".
\par Examples
The following example instructs plumed to calculate the total coordination number of the atoms in group 1-10 with the atoms in group 20-100. For atoms 1-10 coordination numbers are calculated that count the number of atoms from the second group that are within 0.3 nm of the central atom. A neighbour list is used to make this calculation faster, this neighbour list is updated every 100 steps.
-\verbatim
+\plumedfile
COORDINATION GROUPA=1-10 GROUPB=20-100 R_0=0.3 NLIST NL_CUTOFF=0.5 NL_STRIDE=100
-\endverbatim
+\endplumedfile
The following is a dummy example which should compute the value 0 because the self interaction
of atom 1 is skipped. Notice that in plumed 2.0 "self interactions" were not skipped, and the
same calculation should return 1.
-\verbatim
+\plumedfile
c: COORDINATION GROUPA=1 GROUPB=1 R_0=0.3
PRINT ARG=c STRIDE=10
-\endverbatim
-
-\verbatim
-c1: COORDINATION GROUPA=1-10 GROUPB=1-10 R_0=0.3
-x: COORDINATION GROUPA=1-10 R_0=0.3
+\endplumedfile
+
+Here's an example that shows what happens when providing COORDINATION with
+a single group:
+\plumedfile
+# define some huge group:
+group: GROUP ATOMS=1-1000
+# Here's coordination of a group against itself:
+c1: COORDINATION GROUPA=group GROUPB=group R_0=0.3
+# Here's coordination within a single group:
+x: COORDINATION GROUPA=group R_0=0.3
+# This is just multiplying times 2 the variable x:
c2: COMBINE ARG=x COEFFICIENTS=2
+
# the two variables c1 and c2 should be identical, but the calculation of c2 is twice faster
-# since it runs on half of the pairs. Notice that to get the same result you
-# should double it
+# since it runs on half of the pairs.
PRINT ARG=c1,c2 STRIDE=10
-\endverbatim
-See also \ref PRINT and \ref COMBINE
+\endplumedfile
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 23ed21d58dfdd50636fa2f4f1f6d35a461b42b1b..d13aeecdc5ae174ef36b45e7029061d8db15bded 100644
--- a/src/colvar/DHEnergy.cpp
+++ b/src/colvar/DHEnergy.cpp
@@ -56,12 +56,11 @@ Notice that if there are common atoms between GROUPA and GROUPB their interactio
\par Examples
-\verbatim
+\plumedfile
# this is printing the electrostatic interaction between two groups of atoms
dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0
PRINT ARG=dh
-\endverbatim
-(see also \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/DRMSD.cpp b/src/colvar/DRMSD.cpp
index 5a3152ad452872f5115e30558eb709817a259e3e..49efb882ad8db179c4fe19e6545fd03dec9300c7 100644
--- a/src/colvar/DRMSD.cpp
+++ b/src/colvar/DRMSD.cpp
@@ -65,15 +65,15 @@ the positions of the atoms in the reference file and their instantaneous
position. Only pairs of atoms whose distance in the reference structure is within
0.1 and 0.8 nm are considered.
-\verbatim
+\plumedfile
DRMSD REFERENCE=file.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8
-\endverbatim
+\endplumedfile
The following tells plumed to calculate a DRMSD value for a pair of molecules.
-\verbatim
+\plumedfile
DRMSD REFERENCE=file.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 TYPE=INTER-DRMSD
-\endverbatim
+\endplumedfile
In the input reference file (file.pdb) the atoms in each of the two molecules are separated by a TER
command as shown below.
diff --git a/src/colvar/Dimer.cpp b/src/colvar/Dimer.cpp
index 827c843654c28946db8a0c5bae9618a821c39ccd..baead008e84b7b611fc71e5aed2f5cfa8f139417 100644
--- a/src/colvar/Dimer.cpp
+++ b/src/colvar/Dimer.cpp
@@ -85,43 +85,43 @@ the temperature of the system.
This line tells Plumed to compute the Dimer interaction energy for every dimer in the system.
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
-\endverbatim
+\endplumedfile
If the simulation doesn't use virtual sites for the dimers centers of mass,
Plumed has to know in order to determine correctly the total number of dimers from
the total number of atoms:
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES
-\endverbatim
+\endplumedfile
The NOVSITES flag is not required if one provides the atom serial of each Dimer. This is
defined as the atom serial of the first bead of the dimer and is thus a number between 1 and N.
Along with the ATOMS list also the number N of lines describing the first beads has to be given.
For example, the Dimer interaction energy of dimers 1,5,7 is:
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 NATOMS=N ATOMS=1,5,7 DSIGMA=0.002
-\endverbatim
+\endplumedfile
In a Replica Exchange simulation the keyword DSIGMA can be used in two ways:
if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value,
like in the previous examples, and each replica will read its own DSIGMA value. If
a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica.
For 4 replicas:
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 NATOMS=N ATOMS=1,5,7 DSIGMA=0.002,0.002,0.004,0.01
-\endverbatim
+\endplumedfile
\par Usage of the CV
The dimer interaction is not coded in the driver program and has to be inserted
in the hamiltonian of the system as a linear RESTRAINT (see \ref RESTRAINT):
-\verbatim
+\plumedfile
dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002
RESTRAINT ARG=dim AT=0 KAPPA=0 SLOPE=1 LABEL=dimforces
-\endverbatim
+\endplumedfile
In a replica exchange, Metadynamics (see \ref METAD) can be used on the Dimer CV to reduce
the number of replicas. Just keep in mind that METAD SIGMA values should be tuned
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 09a4a6580032fcc3a05bc04fa41d878e54c5bddd..3cffa3553e0bda7c637c26b7aa7e607918d1a5d1 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -37,11 +37,10 @@ Calculate the dipole moment for a group of atoms.
\par Examples
The following tells plumed to calculate the dipole of the group of atoms containing
the atoms from 1-10 and print it every 5 steps
-\verbatim
+\plumedfile
d: DIPOLE GROUP=1-10
PRINT FILE=output STRIDE=5 ARG=5
-\endverbatim
-(see also \ref PRINT)
+\endplumedfile
\attention
If the total charge Q of the group in non zero, then a charge Q/N will be subtracted to every atom,
diff --git a/src/colvar/Distance.cpp b/src/colvar/Distance.cpp
index c3a981771540c28700c91715d06095fc097667f5..279961b7644759ed2012949b7c0b6037e88880fc 100644
--- a/src/colvar/Distance.cpp
+++ b/src/colvar/Distance.cpp
@@ -49,46 +49,44 @@ better to use SCALED_COMPONENTS.
The following input tells plumed to print the distance between atoms 3 and 5,
the distance between atoms 2 and 4 and the x component of the distance between atoms 2 and 4.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=3,5
d2: DISTANCE ATOMS=2,4
d2c: DISTANCE ATOMS=2,4 COMPONENTS
PRINT ARG=d1,d2,d2c.x
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
The following input computes the end-to-end distance for a polymer
of 100 atoms and keeps it at a value around 5.
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5
-\endverbatim
-(See also \ref WHOLEMOLECULES and \ref RESTRAINT).
+\endplumedfile
Notice that NOPBC is used
to be sure that if the end-to-end distance is larger than half the simulation
box the distance is compute properly. Also notice that, since many MD
codes break molecules across cell boundary, it might be necessary to
use the \ref WHOLEMOLECULES keyword (also notice that it should be
-_before_ distance). The list of atoms provided to WHOLEMOLECULES
+_before_ distance). The list of atoms provided to \ref WHOLEMOLECULES
here contains all the atoms between 1 and 100. Strictly speaking, this
is not necessary. If you know for sure that atoms with difference in
the index say equal to 10 are _not_ going to be farther than half cell
you can e.g. use
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1,10,20,30,40,50,60,70,80,90,100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5
-\endverbatim
-Just be sure that the ordered list provide to WHOLEMOLECULES has the following
+\endplumedfile
+Just be sure that the ordered list provide to \ref WHOLEMOLECULES has the following
properties:
- Consecutive atoms should be closer than half-cell throughout the entire simulation.
- Atoms required later for the distance (e.g. 1 and 100) should be included in the list
The following example shows how to take into account periodicity e.g.
in z-component of a distance
-\verbatim
+\plumedfile
# this is a center of mass of a large group
c: COM ATOMS=1-100
# this is the distance between atom 101 and the group
@@ -99,8 +97,7 @@ d: DISTANCE ATOMS=c,101 COMPONENTS
dz: COMBINE ARG=d.z PERIODIC=-10,10
# metadynamics on dd
METAD ARG=dz SIGMA=0.1 HEIGHT=0.1 PACE=200
-\endverbatim
-(see also \ref COM, \ref COMBINE, and \ref METAD)
+\endplumedfile
Using SCALED_COMPONENTS this problem should not arise because they are always periodic
with domain (-0.5,+0.5).
diff --git a/src/colvar/ERMSD.cpp b/src/colvar/ERMSD.cpp
index 3602df0868737aa018969fa45be49a32715501b4..fb5ff6cada2e84ba9d984722777ea0800c038417 100644
--- a/src/colvar/ERMSD.cpp
+++ b/src/colvar/ERMSD.cpp
@@ -84,9 +84,9 @@ for a multi molecular system.
Calculate the eRMSD from reference structure reference.pdb using the default cutoff (2.4). The list of residues involved in the calculation has to be specified. In this example, the eRMSD is calculated
considering residues 1,2,3,4,5,6.
-\verbatim
+\plumedfile
eRMSD1: ERMSD REFERENCE=reference.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index 11e2532e0eeda83f0f4eb086bf744f49de34fb75..4b3f80736ef2a5d93163943604469821e9c4d9e5 100644
--- a/src/colvar/Energy.cpp
+++ b/src/colvar/Energy.cpp
@@ -48,11 +48,10 @@ using GROMACS with lambda replica exchange of with plumed-hrex branch.
\par Examples
The following input instructs plumed to print the energy of the system
-\verbatim
-ENERGY LABEL=ene
+\plumedfile
+ene: ENERGY
PRINT ARG=ene
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Fake.cpp b/src/colvar/Fake.cpp
index 70bd7f278968c9192bba197ca87ee524a5eaecd0..20d70aed9ab5a93e06457ba15c75fc79f15e50ea 100644
--- a/src/colvar/Fake.cpp
+++ b/src/colvar/Fake.cpp
@@ -39,10 +39,9 @@ and just support input and period definition
\par Examples
-\verbatim
+\plumedfile
FAKE ATOMS=1 PERIODIC=-3.14,3.14 LABEL=d2
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/FretEfficiency.cpp b/src/colvar/FretEfficiency.cpp
index 02600e10574cd08165d4f82ac203dabc910f778c..e6f1494529cf9ccf5df2d718e44c798d180f7e9f 100644
--- a/src/colvar/FretEfficiency.cpp
+++ b/src/colvar/FretEfficiency.cpp
@@ -51,22 +51,20 @@ boundary conditions. This behavior can be changed with the NOPBC flag.
The following input tells plumed to print the FRET efficiencies
calculated as a function of the distance between atoms 3 and 5 and
the distance between atoms 2 and 4.
-\verbatim
+\plumedfile
fe1: FRET ATOMS=3,5 R0=5.5
fe2: FRET ATOMS=2,4 R0=5.5
PRINT ARG=fe1,fe2
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
The following input computes the FRET efficiency calculated on the
terminal atoms of a polymer
of 100 atoms and keeps it at a value around 0.5.
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-100
fe: FRET ATOMS=1,100 R0=5.5 NOPBC
RESTRAINT ARG=fe KAPPA=100 AT=0.5
-\endverbatim
-(See also \ref WHOLEMOLECULES and \ref RESTRAINT).
+\endplumedfile
Notice that NOPBC is used
to be sure that if the distance is larger than half the simulation
diff --git a/src/colvar/Gyration.cpp b/src/colvar/Gyration.cpp
index 791f6a3ed81b0f950c5f430218ee545887703201..3764ad404bef8faf64af02476b36038a9780d475 100644
--- a/src/colvar/Gyration.cpp
+++ b/src/colvar/Gyration.cpp
@@ -75,11 +75,10 @@ periodic image.
The following input tells plumed to print the radius of gyration of the
chain containing atoms 10 to 20.
-\verbatim
+\plumedfile
GYRATION TYPE=RADIUS ATOMS=10-20 LABEL=rg
PRINT ARG=rg STRIDE=1 FILE=colvar
-\endverbatim
-(See also \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Implicit.cpp b/src/colvar/Implicit.cpp
index ad53f243cbfd352570d46de5a569ebb354181ac3..b43b3ad604fdaf0f41136d639180fcc0d889cd45 100644
--- a/src/colvar/Implicit.cpp
+++ b/src/colvar/Implicit.cpp
@@ -58,7 +58,7 @@ where \f$\Delta G^\mathrm{free}_i\f$ is the solvation free energy of the isolate
The output from this collective variable, the free energy of solvation, can be used with the \ref BIASVALUE keyword to provide implicit solvation to a system. All parameters are designed to be used with a modified CHARMM36 force field. It takes only non-hydrogen atoms as input, these can be conveniently specified using the \ref GROUP action with the NDX_GROUP parameter. To speed up the calculation, IMPLICIT internally uses a neighbourlist with a cutoff dependent on the type of atom (maximum of 1.95 nm). This cutoff can be extended further by using the NL_BUFFER keyword.
\par Examples
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
WHOLEMOLECULES ENTITY0=1-111
@@ -72,8 +72,7 @@ solv: IMPLICIT ATOMS=protein-h NL_STRIDE=10 NL_BUFFER=0.2
bias: BIASVALUE ARG=solv
PRINT ARG=solv FILE=SOLV
-\endverbatim
-(see also \ref PRINT, \ref GROUP, \ref MOLINFO, \ref WHOLEMOLECULES)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/Jcoupling.cpp b/src/colvar/Jcoupling.cpp
index d192b8bbd6e58c6a039a1796822861b606fba64a..8d8975f91b1e281616f5429546df8c0606a88e9b 100644
--- a/src/colvar/Jcoupling.cpp
+++ b/src/colvar/Jcoupling.cpp
@@ -62,7 +62,7 @@ In the following example we calculate the Ha-N J-coupling from a set of atoms in
dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental datapoints and compute
the correlation and other measures and finally print the results.
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
WHOLEMOLECULES ENTITY0=1-111
@@ -81,11 +81,7 @@ JCOUPLING ...
jhanst: STATS ARG=(jhan\.j_.*) PARARG=(jhan\.exp_.*)
PRINT ARG=jhanst.*,jhan.* FILE=COLVAR STRIDE=100
-
-ENDPLUMED
-
-\endverbatim
-(See also \ref PRINT, \ref STATS)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/MultiRMSD.cpp b/src/colvar/MultiRMSD.cpp
index 7656c232be81b77c7a7220a3babe19ed77aa217b..4cf4ff08bfcdf0424ad531bfa4ef7525524f59e4 100644
--- a/src/colvar/MultiRMSD.cpp
+++ b/src/colvar/MultiRMSD.cpp
@@ -99,17 +99,17 @@ The following tells plumed to calculate the RMSD distance between
the positions of the atoms in the reference file and their instantaneous
position. The Kearseley algorithm for each of the domains.
-\verbatim
+\plumedfile
MULTI-RMSD REFERENCE=file.pdb TYPE=MULTI-OPTIMAL
-\endverbatim
+\endplumedfile
The following tells plumed to calculate the RMSD distance btween the positions of
the atoms in the domains of reference the reference structure and their instantaneous
positions. Here distances are calculated using the \ref DRMSD measure.
-\verbatim
+\plumedfile
MULTI-RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
-\endverbatim
+\endplumedfile
in this case it is possible to use the following DRMSD options in the pdb file using the REMARK syntax:
\verbatim
diff --git a/src/colvar/NOE.cpp b/src/colvar/NOE.cpp
index 82d2b4372a6a885f014351df0ba950be6d50d8b3..b46bd65978621d4098392dd7b86db172f71370f8 100644
--- a/src/colvar/NOE.cpp
+++ b/src/colvar/NOE.cpp
@@ -52,7 +52,7 @@ In the following examples three noes are defined, the first is calculated based
of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances
4-15,4-16,8-15,8-16.
-\verbatim
+\plumedfile
NOE ...
GROUPA1=1,3 GROUPB1=2,2
GROUPA2=5 GROUPB2=7
@@ -61,8 +61,7 @@ LABEL=noes
... NOE
PRINT ARG=noes.* FILE=colvar
-\endverbatim
-(See also \ref PRINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PCARMSD.cpp b/src/colvar/PCARMSD.cpp
index f5d1cf6f2cd4451d6313d68d545cb774d0dc41ca..02861e10963e49e08558e9ce991e7a34e695a866 100644
--- a/src/colvar/PCARMSD.cpp
+++ b/src/colvar/PCARMSD.cpp
@@ -57,9 +57,9 @@ Note that beta and occupancy values in the pdb are neglected and all the weights
\par Examples
-\verbatim
+\plumedfile
PCARMSD AVERAGE=file.pdb EIGENVECTORS=eigenvectors.pdb
-\endverbatim
+\endplumedfile
The input is taken so to be compatible with the output you get from g_covar utility of gromacs (suitably adapted to have a pdb input format).
diff --git a/src/colvar/PRE.cpp b/src/colvar/PRE.cpp
index 906826b1f514fe8a04a073e0c31f998e4af06544..82c94eee23f3a4f10465b27cabc5b537ef209ba8 100644
--- a/src/colvar/PRE.cpp
+++ b/src/colvar/PRE.cpp
@@ -47,7 +47,7 @@ In the following example five PRE intensities are calculated using the distance
oxigen of the spin label and the backbone hydrogens. Omega is the NMR frequency, RTWO the
R2 for the hydrogens, INEPT of 8 ms for the experiment and a TAUC of 1.21 ns
-\verbatim
+\plumedfile
PRE ...
LABEL=HN_pre
INEPT=8
@@ -63,7 +63,7 @@ GROUPA5=451 RTWO5=0.0086341843
PRINT ARG=HN_pre.* FILE=PRE.dat STRIDE=1
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index cdfd96ee1d2a1f025a451e7e1df1889cff42afb5..17567f2d42b4001705bc34a895eb12de98db6fb1 100644
--- a/src/colvar/PathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -42,10 +42,10 @@ in input ("sss" component) and the distance from them ("zzz" component).
Here below is a case where you have defined three frames and you want to
calculate the progress along the path and the distance from it in p1
-\verbatim
+\plumedfile
p1: PATHMSD REFERENCE=file.pdb LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8
PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but
recommended for performance) and states that the neighbor list will be calculated every 4
diff --git a/src/colvar/Position.cpp b/src/colvar/Position.cpp
index a381e039e08212c6fac510c7e4b6ec5532cead40..b66ae5e6ca03a37de32414e7d5a442600ef36bb5 100644
--- a/src/colvar/Position.cpp
+++ b/src/colvar/Position.cpp
@@ -54,14 +54,12 @@ This can be done e.g. using \ref FIT_TO_TEMPLATE.
\par Examples
-\verbatim
+\plumedfile
# align to a template
FIT_TO_TEMPLATE REFERENCE=ref.pdb
p: POSITION ATOM=3
PRINT ARG=p.x,p.y,p.z
-\endverbatim
-(see also \ref FIT_TO_TEMPLATE)
-
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index a8a21fef2057803070dd7dc3a46aee30ad62a7ac..eb1c27f0255a2b44d1482133ff2993e57cd3dc99 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -46,10 +46,10 @@ where the parameters \f$X_i\f$ and \f$Y_i\f$ are provided in the input pdb (al
\f$D_i(x)\f$ is the MSD after optimal alignment calculated on the pdb frames you input (see Kearsley).
\par Examples
-\verbatim
+\plumedfile
p3: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4
PRINT ARG=p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighborlist parameter (optional but
recommended for performance) and states that the neighbor list will be calculated every 4
diff --git a/src/colvar/Puckering.cpp b/src/colvar/Puckering.cpp
index b90bdfbc4c732f6bb69932e7c4ddc7d68d17a0cf..66edb54c5d0e3fd1fa476cee61d43676782097c7 100644
--- a/src/colvar/Puckering.cpp
+++ b/src/colvar/Puckering.cpp
@@ -60,11 +60,11 @@ namespace colvar {
\par Examples
This input tells plumed to print the puckering phase angle of the 3rd nucleotide of a RNA molecule on file COLVAR.
- \verbatim
+ \plumedfile
MOLINFO STRUCTURE=rna.pdb MOLTYPE=rna
PUCKERING ATOMS=@sugar-3 LABEL=puck
PRINT ARG=puck.phs FILE=COLVAR
- \endverbatim
+ \endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/RDC.cpp b/src/colvar/RDC.cpp
index 18db380141d62a7dc45c604a662c9451abb5e9bf..43dc4c1ee3f563989c03d597b7e74b007361cc7e 100644
--- a/src/colvar/RDC.cpp
+++ b/src/colvar/RDC.cpp
@@ -94,7 +94,7 @@ respect to a set of experimental data is calculated and restrained. In addition,
and only for analysis purposes, the same RDCs are calculated using a Single Value
Decomposition algorithm.
-\verbatim
+\plumedfile
RDC ...
GYROM=-72.5388
SCALE=1.0
@@ -124,8 +124,7 @@ LABEL=svd
PRINT ARG=nh.corr,rdce.bias FILE=colvar
PRINT ARG=svd.* FILE=svd
-\endverbatim
-(See also \ref PRINT, \ref RESTRAINT)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index 8801dfeed200153fcd9368e4e72cbaff987774e5..bbc16bc468c2eea9685165d28e5da089931f3e3a 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -105,6 +105,7 @@ you really know what you are doing however as the results can be rather strange.
In PDB files the atomic coordinates and box lengths should be in Angstroms unless
you are working with natural units. If you are working with natural units then the coordinates
should be in your natural length unit. For more details on the PDB file format visit http://www.wwpdb.org/docs.html.
+Make sure your PDB file is correclty formatted as explained \ref pdbreader "in this page".
A different method is used to calculate the RMSD distance when you use TYPE=OPTIMAL on the input line. In this case the root mean square
deviation is calculated after the positions of geometric centers in the reference and instantaneous configurations are aligned AND after
@@ -133,9 +134,9 @@ The following tells plumed to calculate the RMSD distance between
the positions of the atoms in the reference file and their instantaneous
position. The Kearseley algorithm is used so this is done optimally.
-\verbatim
+\plumedfile
RMSD REFERENCE=file.pdb TYPE=OPTIMAL
-\endverbatim
+\endplumedfile
...
diff --git a/src/colvar/Template.cpp b/src/colvar/Template.cpp
index 85cb95d27ec8837ed4b37a8cf64ec4508b6c0aa8..6fb3c58451c46dc18ee631315692c5920f2e1df4 100644
--- a/src/colvar/Template.cpp
+++ b/src/colvar/Template.cpp
@@ -40,11 +40,11 @@ This file provides a template for if you want to introduce a new CV.
<!---You should put an example of how to use your CV here--->
-\verbatim
+\plumedfile
# This should be a sample input.
t: TEMPLATE ATOMS=1,2
PRINT ARG=t STRIDE=100 FILE=COLVAR
-\endverbatim
+\endplumedfile
<!---You should reference here the other actions used in this example--->
(see also \ref PRINT)
diff --git a/src/colvar/Torsion.cpp b/src/colvar/Torsion.cpp
index 274d0565a424354ef9a8d88ec84edd6037e8859a..4b697b06976c3bdc7508a4961a2c6f4d58b8dc00 100644
--- a/src/colvar/Torsion.cpp
+++ b/src/colvar/Torsion.cpp
@@ -43,23 +43,23 @@ orthogonal to an axis.
This input tells plumed to print the torsional angle between atoms 1, 2, 3 and 4
on file COLVAR.
-\verbatim
+\plumedfile
t: TORSION ATOMS=1,2,3,4
# this is an alternative, equivalent, definition:
# t: TORSION VECTOR1=2,1 AXIS=2,3 VECTOR2=3,4
PRINT ARG=t FILE=COLVAR
-\endverbatim
+\endplumedfile
If you are working with a protein you can specify the special named torsion angles \f$\phi\f$, \f$\psi\f$, \f$\omega\f$ and \f$\chi_1\f$
by using TORSION in combination with the \ref MOLINFO command. This can be done by using the following
syntax.
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
PRINT ARG=t1,t2 FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/colvar/Volume.cpp b/src/colvar/Volume.cpp
index 7b4fb9aacf87a9fbf5b8e39693e4aff71f9eb22d..837f6ce75871ad84840e8ea1d5be7a20dee2bc77 100644
--- a/src/colvar/Volume.cpp
+++ b/src/colvar/Volume.cpp
@@ -36,11 +36,10 @@ Calculate the volume of the simulation box.
\par Examples
The following input tells plumed to print the volume of the system
-\verbatim
-VOLUME LABEL=vol
+\plumedfile
+vol: VOLUME
PRINT ARG=vol
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Fccubic.cpp b/src/crystallization/Fccubic.cpp
index fc1793ab39cea57d52603652660a35153aa5761e..47154f4c6f7d393c605f85a0a656b1da4717fe0c 100644
--- a/src/crystallization/Fccubic.cpp
+++ b/src/crystallization/Fccubic.cpp
@@ -63,10 +63,10 @@ so on. Notice also that you can rotate the reference frame if you are using a n
The following input calculates the FCCUBIC parameter for the 64 atoms in the system
and then calculates and prints the average value for this quantity.
-\verbatim
+\plumedfile
FCCUBIC SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=d
PRINT ARG=d.* FILE=colv
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Gradient.cpp b/src/crystallization/Gradient.cpp
index 173d9e5adb0afbfe84d18ee5c22e13f4a089db57..e3af25856de604e00803a5a136a57895590263c7 100644
--- a/src/crystallization/Gradient.cpp
+++ b/src/crystallization/Gradient.cpp
@@ -39,22 +39,22 @@ The input below calculates the gradient of the density of atoms in the manner
described in \cite fede-grad in order to detect whether or not atoms are distributed
uniformly along the x-axis of the simulation cell.
-\verbatim
+\plumedfile
d1: DENSITY SPECIES=1-50
s1: GRADIENT ORIGIN=1 DATA=d1 DIR=x NBINS=4 SIGMA=1.0
PRINT ARG=s1 FILE=colvar
-\endverbatim
+\endplumedfile
The input below calculates the coordination numbers of the 50 atoms in the simulation cell.
The gradient of this quantity is then evaluated in the manner described using the equation above
to detect whether the average values of the coordination number are uniformly distributed along the
x-axis of the simulation cell.
-\verbatim
+\plumedfile
d2: COORDINATIONNUMBER SPECIES=1-50 SWITCH={RATIONAL R_0=2.0} MORE_THAN={EXP R_0=4.0}
s2: GRADIENT ORIGIN=1 DATA=d2 DIR=x NBINS=4 SIGMA=1.0
PRINT ARG=s2 FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/InterMolecularTorsions.cpp b/src/crystallization/InterMolecularTorsions.cpp
index 3839e094d6793285e2f3909fe557b0d656562fa7..58294492f6fa982d8463e5cc476f5dde4a74080c 100644
--- a/src/crystallization/InterMolecularTorsions.cpp
+++ b/src/crystallization/InterMolecularTorsions.cpp
@@ -64,12 +64,12 @@ between the two molecules. As such the torsional angles between molecules that
histogram while the torsional angles between molecules that are far apart does not contribute to the histogram. The histogram is
averaged over the whole trajectory and output once all the trajectory frames have been read.
-\verbatim
+\plumedfile
m1: MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8
tt_p: INTERMOLECULARTORSIONS MOLS=m1 SWITCH={RATIONAL R_0=0.25 D_0=2.0 D_MAX=3.0}
htt_p: HISTOGRAM DATA=tt_p GRID_MIN=-pi GRID_MAX=pi BANDWIDTH=0.1 GRID_BIN=200 STRIDE=1
DUMPGRID GRID=htt_p FILE=myhist.out
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/MoleculeOrientation.cpp b/src/crystallization/MoleculeOrientation.cpp
index 5bade7022c81bbdc6b6a391f4723cf704daee5e5..6001f6f095c25bd9d16b7acc0ab9f23c14252df1 100644
--- a/src/crystallization/MoleculeOrientation.cpp
+++ b/src/crystallization/MoleculeOrientation.cpp
@@ -39,10 +39,10 @@ The following input tells plumed to calculate the distances between two of the a
This is done for the same set of atoms four different molecules and the average separation is then
calculated.
-\verbatim
+\plumedfile
MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8 MEAN LABEL=mm
PRINT ARG=mm.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
diff --git a/src/crystallization/Q3.cpp b/src/crystallization/Q3.cpp
index 6c3aeedc2f6f8d2fbfe9606e4d37f50e144535af..038115a92158389807b110c24ea959e6785c31c7 100644
--- a/src/crystallization/Q3.cpp
+++ b/src/crystallization/Q3.cpp
@@ -60,28 +60,28 @@ the \f$q_{3}\f$ vectors on adjacent atoms. More information on these variables
The following command calculates the average Q3 parameter for the 64 atoms in a box of Lennard Jones and prints this
quantity to a file called colvar:
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q3
PRINT ARG=q3.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the histogram of Q3 parameters for the 64 atoms in a box of Lennard Jones and prints these
quantities to a file called colvar:
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q3
PRINT ARG=q3.* FILE=colvar
-\endverbatim
+\endplumedfile
The following command could be used to measure the Q3 paramters that describe the arrangement of chlorine ions around the
sodium atoms in NaCl. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input
with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions. Once again the average Q3 paramter is calculated and output to a
file called colvar
-\verbatim
+\plumedfile
Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q3
PRINT ARG=q3.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
@@ -136,30 +136,30 @@ adjacent atoms is correlated.
The following command calculates the average value of the LOCAL_Q3 parameter for the 64 Lennard Jones atoms in the system under study and prints this
quantity to a file called colvar.
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q3
LOCAL_Q3 ARG=q3 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq3
PRINT ARG=lq3.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following input calculates the distribution of LOCAL_Q3 parameters at any given time and outputs this information to a file.
-\verbatim
+\plumedfile
Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q3
LOCAL_Q3 ARG=q3 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq3
PRINT ARG=lq3.* FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates the LOCAL_Q3 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere
are done with those of all the other atoms in the system. The final quantity is the average and is outputted to a file
-\verbatim
+\plumedfile
Q3 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q3a
Q3 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q3b
LOCAL_Q3 ARG=q3a,q3b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w3
PRINT ARG=w3.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Q4.cpp b/src/crystallization/Q4.cpp
index fa76b0d10e762b3b2efd30382c0ca09cfdc35670..a4f7d327b2545848609996a8d2fab50965a9616e 100644
--- a/src/crystallization/Q4.cpp
+++ b/src/crystallization/Q4.cpp
@@ -60,28 +60,28 @@ the \f$q_{4}\f$ vectors on adjacent atoms. More information on these variables
The following command calculates the average Q4 parameter for the 64 atoms in a box of Lennard Jones and prints this
quantity to a file called colvar:
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q4
PRINT ARG=q4.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the histogram of Q4 parameters for the 64 atoms in a box of Lennard Jones and prints these
quantities to a file called colvar:
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q4
PRINT ARG=q4.* FILE=colvar
-\endverbatim
+\endplumedfile
The following command could be used to measure the Q4 paramters that describe the arrangement of chlorine ions around the
sodium atoms in NaCl. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input
with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions. Once again the average Q4 paramter is calculated and output to a
file called colvar
-\verbatim
+\plumedfile
Q4 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q4
PRINT ARG=q4.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
@@ -136,30 +136,30 @@ adjacent atoms is correlated.
The following command calculates the average value of the LOCAL_Q4 parameter for the 64 Lennard Jones atoms in the system under study and prints this
quantity to a file called colvar.
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q4
LOCAL_Q4 ARG=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq4
PRINT ARG=lq4.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following input calculates the distribution of LOCAL_Q4 parameters at any given time and outputs this information to a file.
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q4
LOCAL_Q4 ARG=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq4
PRINT ARG=lq4.* FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates the LOCAL_Q4 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere
are done with those of all the other atoms in the system. The final quantity is the average and is outputted to a file
-\verbatim
+\plumedfile
Q4 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q4a
Q4 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q4b
LOCAL_Q4 ARG=q4a,q4b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w4
PRINT ARG=w4.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Q6.cpp b/src/crystallization/Q6.cpp
index 447b0e1cb42d6ec71c558e22be071f1773586d93..a848174ab88fbee83044c3488cbec611d3e8f190 100644
--- a/src/crystallization/Q6.cpp
+++ b/src/crystallization/Q6.cpp
@@ -60,28 +60,28 @@ the \f$q_{6}\f$ vectors on adjacent atoms. More information on these variables
The following command calculates the average Q6 parameter for the 64 atoms in a box of Lennard Jones and prints this
quantity to a file called colvar:
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q6
PRINT ARG=q6.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the histogram of Q6 parameters for the 64 atoms in a box of Lennard Jones and prints these
quantities to a file called colvar:
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q6
PRINT ARG=q6.* FILE=colvar
-\endverbatim
+\endplumedfile
The following command could be used to measure the Q6 paramters that describe the arrangement of chlorine ions around the
sodium atoms in NaCl. The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input
with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions. Once again the average Q6 paramter is calculated and output to a
file called colvar
-\verbatim
+\plumedfile
Q6 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q6
PRINT ARG=q6.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
@@ -136,30 +136,30 @@ adjacent atoms is correlated.
The following command calculates the average value of the LOCAL_Q6 parameter for the 64 Lennard Jones atoms in the system under study and prints this
quantity to a file called colvar.
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q6
LOCAL_Q6 ARG=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq6
PRINT ARG=lq6.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following input calculates the distribution of LOCAL_Q6 parameters at any given time and outputs this information to a file.
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q6
LOCAL_Q6 ARG=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq6
PRINT ARG=lq6.* FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates the LOCAL_Q6 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere
are done with those of all the other atoms in the system. The final quantity is the average and is outputted to a file
-\verbatim
+\plumedfile
Q6 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q6a
Q6 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q6b
LOCAL_Q6 ARG=q4a,q4b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w4
PRINT ARG=w6.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/SMAC.cpp b/src/crystallization/SMAC.cpp
index ce83df73808be7d532e308f945b942590e0a5b68..3d7085a979e6979fe76d70b420e2f8fa8aad17cf 100644
--- a/src/crystallization/SMAC.cpp
+++ b/src/crystallization/SMAC.cpp
@@ -65,7 +65,7 @@ the indices of three atoms for each of the MOL keywords below we are telling PLU
numbers to determine the orientation of the molecule that will ultimately be used when calculating the \f$\theta_{ij}\f$
terms in the formula above. The atom with the third index meanwhile is used when we calculate \f$r_{ij}\f$.
-\verbatim
+\plumedfile
MOLECULES ...
MOL1=9,10,9
MOL2=89,90,89
@@ -86,13 +86,13 @@ SMAC ...
... SMAC
PRINT ARG=s2.* FILE=colvar
-\endverbatim
+\endplumedfile
This second example works in a way that is very similar to the previous command. Now, however,
the orientation of the molecules is determined by finding the plane that contains the positions
of three atoms.
-\verbatim
+\plumedfile
PLANES ...
MOL1=9,10,11
MOL2=89,90,91
@@ -114,7 +114,7 @@ SMAC ...
... SMAC
PRINT ARG=s2.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/SimpleCubic.cpp b/src/crystallization/SimpleCubic.cpp
index 4d50cc7d59a408b9f138385d736d1d430b941512..2c15767c272aad5c6a60f595cccd39a86d1c60e8 100644
--- a/src/crystallization/SimpleCubic.cpp
+++ b/src/crystallization/SimpleCubic.cpp
@@ -55,15 +55,15 @@ so on. Notice also that you can rotate the reference frame if you are using a n
The following input tells plumed to calculate the simple cubic parameter for the atoms 1-100 with themselves.
The mean value is then calculated.
-\verbatim
+\plumedfile
SIMPLECUBIC SPECIES=1-100 R_0=1.0 MEAN
-\endverbatim
+\endplumedfile
The following input tells plumed to look at the ways atoms 1-100 are within 3.0 are arranged about atoms
from 101-110. The number of simple cubic parameters that are greater than 0.8 is then output
-\verbatim
+\plumedfile
SIMPLECUBIC SPECIESA=101-110 SPECIESB=1-100 R_0=3.0 MORE_THAN={RATIONAL R_0=0.8 NN=6 MM=12 D_0=0}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/crystallization/Tetrahedral.cpp b/src/crystallization/Tetrahedral.cpp
index 616cf766bf1bc8ebdbcbede38aa94a8d0d4cb4b0..87c6e33ae87d942c012716bdcfc272538f20dd58 100644
--- a/src/crystallization/Tetrahedral.cpp
+++ b/src/crystallization/Tetrahedral.cpp
@@ -54,20 +54,20 @@ when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zer
The following command calculates the average value of the tetrahedrality parameter for a set of 64 atoms all of the same type
and outputs this quantity to a file called colvar.
-\verbatim
+\plumedfile
tt: TETRAHEDRAL SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN
PRINT ARG=tt.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following command calculates the number of tetrahedrality parameters that are greater than 0.8 in a set of 10 atoms.
In this calculation it is assumed that there are two atom types A and B and that the first coordination sphere of the
10 atoms of type A contains atoms of type B. The formula above is thus calculated for ten different A atoms and within
it the sum over \f$j\f$ runs over 40 atoms of type B that could be in the first coordination sphere.
-\verbatim
+\plumedfile
tt: TETRAHEDRAL SPECIESA=1-10 SPECIESB=11-40 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MORE_THAN={RATIONAL R_0=0.8}
PRINT ARG=tt.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/eds/EDS.cpp b/src/eds/EDS.cpp
index e5e575abe167259d29c679cefae64ac164f8c5f7..e7e0e4331d1b9c30f2938ae1e1f73cd317f1233e 100644
--- a/src/eds/EDS.cpp
+++ b/src/eds/EDS.cpp
@@ -63,7 +63,7 @@ It is not possible to set the target value of the observable to zero with the de
The following input for a harmonic oscillator of two beads will adaptively find a linear bias to change the mean and variance to the target values. The PRINT line shows how to access the value of the coupling constants.
-\verbatim
+\plumedfile
dist: DISTANCE ATOMS=1,2
# this is the squared of the distance
dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO
@@ -71,19 +71,19 @@ dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO
#bias mean and variance
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0
PRINT ARG=dist,dist2,eds.dist_coupling,eds.dist2_coupling,eds.bias,eds.force2 FILE=colvars.dat STRIDE=100
-\endverbatim
+\endplumedfile
Rather than trying to find the coupling constants adaptively, can ramp up to a constant value.
-\verbatim
+\plumedfile
#ramp couplings from 0,0 to -1,1 over 50000 steps
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 FIXED=-1,1 RAMP PERIOD=50000 TEMP=1.0
#same as above, except starting at -0.5,0.5 rather than default of 0,0
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 FIXED=-1,1 INIT=-0.5,0.5 RAMP PERIOD=50000 TEMP=1.0
-\endverbatim
+\endplumedfile
A restart file can be added to dump information needed to restart/continue simulation using these parameters every STRIDE.
-\verbatim
+\plumedfile
#add the option to write to a restart file
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 OUT_RESTART=restart.dat
@@ -98,7 +98,7 @@ eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.
#add the option to read in a previous restart file and continue the bias, but use the mean from the previous run as the starting point
eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=50000 TEMP=1.0 IN_RESTART=restart.dat MEAN
-\endverbatim
+\endplumedfile
*/
diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
index e76ed7b8bb2339ecdfb18fa5603dcd2eb1ec63e3..62f66e35d81b082325724ee919ba968e72e39d6c 100644
--- a/src/function/Combine.cpp
+++ b/src/function/Combine.cpp
@@ -52,23 +52,23 @@ is periodic.
The following input tells plumed to print the distance between atoms 3 and 5
its square (as computed from the x,y,z components) and the distance
again as computed from the square root of the square.
-\verbatim
+\plumedfile
DISTANCE LABEL=dist ATOMS=3,5 COMPONENTS
COMBINE LABEL=distance2 ARG=dist.x,dist.y,dist.z POWERS=2,2,2 PERIODIC=NO
COMBINE LABEL=distance ARG=distance2 POWERS=0.5 PERIODIC=NO
PRINT ARG=distance,distance2
-\endverbatim
+\endplumedfile
(See also \ref PRINT and \ref DISTANCE).
The following input tells plumed to add a restraint on the
cube of a dihedral angle. Notice that since the angle has a
periodic domain
-pi,pi its cube has a domain -pi**3,pi**3.
-\verbatim
+\plumedfile
t: TORSION ATOMS=1,3,5,7
c: COMBINE ARG=t POWERS=3 PERIODIC=-31.0062766802998,31.0062766802998
RESTRAINT ARG=c KAPPA=10 AT=0
-\endverbatim
+\endplumedfile
diff --git a/src/function/Ensemble.cpp b/src/function/Ensemble.cpp
index 9976c25015d86e42ee3d5ea911d1c2d2c47029db..bc1e05fb28569a74cea4b7b471bae55b784fb950 100644
--- a/src/function/Ensemble.cpp
+++ b/src/function/Ensemble.cpp
@@ -38,12 +38,11 @@ Each collective variable is averaged separately and stored in a component labell
\par Examples
The following input tells plumed to calculate the distance between atoms 3 and 5
and the average it over the available replicas.
-\verbatim
+\plumedfile
dist: DISTANCE ATOMS=3,5
ens: ENSEMBLE ARG=dist
PRINT ARG=dist,ens.dist
-\endverbatim
-(See also \ref PRINT and \ref DISTANCE).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index f4d481d733f1ad840057c769254a3f098642cf85..25a87e7182ba39dcfe26eecf6808a97ad82e096d 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -49,17 +49,17 @@ It is a function of MSD that are obtained by the joint use of MSD variable and S
Here below is a case where you have defined three frames and you want to
calculate the progress alng the path and the distance from it in p1
-\verbatim
+\plumedfile
t1: RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
t2: RMSD REFERENCE=frame_21.dat TYPE=OPTIMAL SQUARED
t3: RMSD REFERENCE=frame_42.dat TYPE=OPTIMAL SQUARED
p1: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0
PRINT ARG=t1,t2,t3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
In this second example is shown how to define a PATH in the \ref CONTACTMAP space:
-\verbatim
+\plumedfile
CONTACTMAP ...
ATOMS1=1,2 REFERENCE1=0.1
ATOMS2=3,4 REFERENCE2=0.5
@@ -92,7 +92,7 @@ CMDIST
p1: FUNCPATHMSD ARG=c1,c2,c3 LAMBDA=500.0
PRINT ARG=c1,c2,c3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index 6e3bd96f689e6001e8e7e4b55bbda0c3a415c2f8..429a5a1436913f1a308dd700a67d8bb5903d742d 100644
--- a/src/function/LocalEnsemble.cpp
+++ b/src/function/LocalEnsemble.cpp
@@ -40,7 +40,7 @@ The following input tells plumed to calculate the chemical shifts for four
different proteins in the same simulation box then average them, calcualated
the sum of the squared deviation with respect to the experiemntal values and
applies a linear restraint.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=data/template.pdb
chaina: GROUP ATOMS=1-1640
@@ -68,7 +68,7 @@ sthn: STATS ARG=(enshn\.csa\.hn_.*) PARARG=(csa\.exphn_.*) SQDEVSUM
stnh: STATS ARG=(ensnh\.csa\.nh_.*) PARARG=(csa\.expnh_.*) SQDEVSUM
res: RESTRAINT ARG=stca.*,stcb.*,stco.*,sthn.*,stnh.* AT=0.,0.,0.,0.,0. KAPPA=0.,0.,0.,0.,0 SLOPE=16.,16.,12.,24.,0.5
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/Matheval.cpp b/src/function/Matheval.cpp
index 59e6e9bf05007580e9ece7b1506a4c55103d3869..d21907e68eb6e92c6533d4755439390a8ee6af41 100644
--- a/src/function/Matheval.cpp
+++ b/src/function/Matheval.cpp
@@ -54,14 +54,14 @@ PLUMED has been linked to it
The following input tells plumed to perform a metadynamics
using as a CV the difference between two distances.
-\verbatim
+\plumedfile
dAB: DISTANCE ARG=10,12
dAC: DISTANCE ARG=10,15
diff: MATHEVAL ARG=dAB,dAC FUNC=y-x PERIODIC=NO
# notice: the previous line could be replaced with the following
# diff: COMBINE ARG=dAB,dAC COEFFICIENTS=-1,1
METAD ARG=diff WIDTH=0.1 HEIGHT=0.5 BIASFACTOR=10 PACE=100
-\endverbatim
+\endplumedfile
(see also \ref DISTANCE, \ref COMBINE, and \ref METAD).
Notice that forces applied to diff will be correctly propagated
to atoms 10, 12, and 15.
@@ -75,7 +75,7 @@ The following input tells plumed to print the angle between vectors
identified by atoms 1,2 and atoms 2,3
its square (as computed from the x,y,z components) and the distance
again as computed from the square root of the square.
-\verbatim
+\plumedfile
DISTANCE LABEL=d1 ATOMS=1,2 COMPONENTS
DISTANCE LABEL=d2 ATOMS=2,3 COMPONENTS
MATHEVAL ...
@@ -86,7 +86,7 @@ MATHEVAL ...
PERIODIC=NO
... MATHEVAL
PRINT ARG=theta
-\endverbatim
+\endplumedfile
(See also \ref PRINT and \ref DISTANCE).
Notice that the matheval library implements a large number of functions (trigonometric, exp, log, etc).
@@ -96,13 +96,13 @@ a straightforward implementation of if clauses.
For example, imagine that you want to implement a restraint that only acts when a
distance is larger than 0.5. You can do it with
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=10,15
m: MATHEVAL ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO
# check the function you are applying:
PRINT ARG=d,n FILE=checkme
RESTRAINT ARG=d AT=0.5 KAPPA=10.0
-\endverbatim
+\endplumedfile
(see also \ref DISTANCE, \ref PRINT, and \ref RESTRAINT)
The meaning of the function `0.5*step(0.5-x)+x*step(x-0.5)` is:
@@ -133,7 +133,7 @@ MATHEVAL can be used in combination with \ref DISTANCE to implement variants of
DISTANCE keyword that were present in PLUMED 1.3 and that allowed to compute
the distance of a point from a line defined by two other points, or the progression
along that line.
-\verbatim
+\plumedfile
# take center of atoms 1 to 10 as reference point 1
p1: CENTER ATOMS=1-10
# take center of atoms 11 to 20 as reference point 2
@@ -156,7 +156,7 @@ fromaxis: MATHEVAL ARG=d13,d23,d12,onaxis VAR=x,y,z,o FUNC=(0.5*(y^2+x^2)-o^2-0.
PRINT ARG=onaxis,fromaxis
-\endverbatim
+\endplumedfile
Notice that these equations have been used to combine \ref RMSD
from different snapshots of a protein so as to define
diff --git a/src/function/Piecewise.cpp b/src/function/Piecewise.cpp
index e0f4bbd52ac4ec5b4eb51c3ab9de53f119a1b9cb..ebd886de09e4c77fb8f2685b8d5dc5d1d50d53b2 100644
--- a/src/function/Piecewise.cpp
+++ b/src/function/Piecewise.cpp
@@ -55,15 +55,14 @@ in a vector of values. Each value will be named as the name of the original
argument with suffix _pfunc.
\par Examples
-\verbatim
+\plumedfile
dist1: DISTANCE ATOMS=1,10
dist2: DISTANCE ATOMS=2,11
pw: PIECEWISE POINT0=1,10 POINT1=1,PI POINT2=3,10 ARG=dist1
ppww: PIECEWISE POINT0=1,10 POINT1=1,PI POINT2=3,10 ARG=dist1,dist2
PRINT ARG=pw,ppww.dist1_pfunc,ppww.dist2_pfunc
-\endverbatim
-(See also \ref PRINT and \ref DISTANCE).
+\endplumedfile
*/
diff --git a/src/function/Sort.cpp b/src/function/Sort.cpp
index f1e9b2a71773a1ab8dc98195e654fc7d29dc9d2a..fc8e4ca233822da29806cd3b87e5809526235367 100644
--- a/src/function/Sort.cpp
+++ b/src/function/Sort.cpp
@@ -43,15 +43,14 @@ labelled <em>label</em>.1, the second lowest will be labelled <em>label</em>.2 a
\par Examples
The following input tells plumed to print the distance of the closest and of
the farthest atoms to atom 1, chosen among atoms from 2 to 5
-\verbatim
+\plumedfile
d12: DISTANCE ATOMS=1,2
d13: DISTANCE ATOMS=1,3
d14: DISTANCE ATOMS=1,4
d15: DISTANCE ATOMS=1,5
sort: SORT ARG=d12,d13,d14,d15
PRINT ARG=sort.1,sort.4
-\endverbatim
-(See also \ref PRINT and \ref DISTANCE).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/Stats.cpp b/src/function/Stats.cpp
index 429442e6d833bc41ea63beb9283d3dd096be5b69..438d8f98b86cede7896a77e57e794ee926ad47a5 100644
--- a/src/function/Stats.cpp
+++ b/src/function/Stats.cpp
@@ -41,13 +41,13 @@ from other actions using PARARG (for example using experimental values from coll
The following input tells plumed to print the distance between three couple of atoms
and compare them with three reference distances.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=10,50
d2: DISTANCE ATOMS=1,100
d3: DISTANCE ATOMS=45,75
st: STATS ARG=d1,d2,d3 PARAMETERS=1.5,4.0,2.0
PRINT ARG=d1,d2,d3,st.*
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/function/Target.cpp b/src/function/Target.cpp
index 5ce91249563a68b9599abf0806d02b3aa7c95f65..1724cf3ff8263b4c40dfc68e4bd9e35ff7a4c3c0 100644
--- a/src/function/Target.cpp
+++ b/src/function/Target.cpp
@@ -75,12 +75,12 @@ specified in the input.
The following input calculates the distance between a reference configuration and the instaneous position of the system in the trajectory.
The position of the reference configuration is specified by providing the values of the distance between atoms 1 and 2 and atoms 3 and 4.
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=3,4
t1: TARGET REFERENCE=myref.pdb TYPE=EUCLIDEAN
PRINT ARG=t1 FILE=colvar
-\endverbatim
+\endplumedfile
The contents of the file containing the reference structure (myref.pdb) is shown below. As you can see you must provide information on the
labels of the CVs that are being used to define the position of the reference configuration in this file together with the values that these
diff --git a/src/generic/Debug.cpp b/src/generic/Debug.cpp
index 742b3b85420f4d77b99907274a3958945d3b1034..36654b0d90fdb901fcdfc15fa027b3f71112c05d 100644
--- a/src/generic/Debug.cpp
+++ b/src/generic/Debug.cpp
@@ -37,12 +37,12 @@ Can be used while debugging or optimizing plumed.
\par Examples
-\verbatim
+\plumedfile
# print detailed (action-by-action) timers at the end of simulation
DEBUG DETAILED_TIMERS
# dump every two steps which are the atoms required from the MD code
DEBUG logRequestedAtoms STRIDE=2
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index d6ee377488219851af8eb407533666d13690548b..5e613cf9a94814542706e3cb10852e3875faf907 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -70,15 +70,23 @@ Notice that gro/xtc/trr files can only contain coordinates in nm.
The following input instructs plumed to print out the positions of atoms
1-10 together with the position of the center of mass of atoms 11-20 every
10 steps to a file called file.xyz.
-\verbatim
+\plumedfile
COM ATOMS=11-20 LABEL=c1
DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1
-\endverbatim
-(see also \ref COM)
+\endplumedfile
+Notice that the coordinates in the xyz file will be expressed in nm, since these
+are the defaults units in PLUMED. If you want the xyz file to be expressed in A, you should use the
+following input
+\plumedfile
+COM ATOMS=11-20 LABEL=c1
+DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1 UNITS=A
+\endplumedfile
+As an alternative, you might want to set all the lentght used by PLUMED to Angstrom using the \ref UNITS
+action. However, this latter choice will affect all your input and output.
The following input is very similar but dumps a .gro (gromacs) file,
which also contains atom and residue names.
-\verbatim
+\plumedfile
# this is required to have proper atom names:
MOLINFO STRUCTURE=reference.pdb
# if omitted, atoms will have "X" name...
@@ -87,8 +95,25 @@ COM ATOMS=11-20 LABEL=c1
DUMPATOMS STRIDE=10 FILE=file.gro ATOMS=1-10,c1
# notice that last atom is a virtual one and will not have
# a correct name in the resulting gro file
-\endverbatim
-(see also \ref COM and \ref MOLINFO)
+\endplumedfile
+
+The `file.gro` will contain coordinates expressed in nm, since this is the convention for gro files.
+
+In case you have compiled PLUMED with `xdrfile` library, you might even write xtc or trr files as follows
+\plumedfile
+COM ATOMS=11-20 LABEL=c1
+DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1
+\endplumedfile
+Notice that xtc files are significantly smaller than gro and xyz files.
+
+Finally, consider that gro and xtc file store coordinates with limited precision set by the
+`PRECISION` keyword. Default value is 3, which means "3 digits after dot" in nm (1/1000 of a nm).
+The following will write a larger xtc file with high resolution coordinates:
+\plumedfile
+COM ATOMS=11-20 LABEL=c1
+DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1 PRECISION=7
+\endplumedfile
+
*/
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index c74343aca0983c529c9521c9d137b271c0c785ad..38c686d7b4aec532684f2ce6f0dcd40f4319520f 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -42,11 +42,11 @@ can be done by outputting the derivatives calculated analytically and numericall
\par Examples
The following input instructs plumed to write a file called deriv that contains both the
analytical and numerical derivatives of the distance between atoms 1 and 2.
-\verbatim
+\plumedfile
DISTANCE ATOM=1,2 LABEL=distance
DISTANCE ATOM=1,2 LABEL=distanceN NUMERICAL_DERIVATIVES
DUMPDERIVATIVES ARG=distance,distanceN STRIDE=1 FILE=deriv
-\endverbatim
+\endplumedfile
(See also \ref DISTANCE)
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index f5e204d65b8297973a50099f9b74797885d788ac..a376de281a1cacc6b5a0b9dd7a0841aa10046309 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -43,12 +43,10 @@ by specifying more than one argument. You can control the buffering of output us
\par Examples
The following input instructs plumed to write a file called forces that contains
the force acting on the distance between atoms 1 and 2.
-\verbatim
+\plumedfile
DISTANCE ATOM=1,2 LABEL=distance
DUMPFORCES ARG=distance STRIDE=1 FILE=forces
-\endverbatim
-
-(See also \ref DISTANCE)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/DumpMassCharge.cpp b/src/generic/DumpMassCharge.cpp
index 4153bc83844773ab00f19ec811be5d704a9f4b3c..25224f3b3c5d643d9e721e5d215a5e874a8df80f 100644
--- a/src/generic/DumpMassCharge.cpp
+++ b/src/generic/DumpMassCharge.cpp
@@ -49,14 +49,13 @@ masses for all atoms are written.
You can add the DUMPMASSCHARGE action at the end of the plumed.dat
file that you use during an MD simulations:
-\verbatim
+\plumedfile
c1: COM ATOMS=1-10
c2: COM ATOMS=11-20
PRINT ARG=c1,c2 FILE=colvar STRIDE=100
DUMPMASSCHARGE FILE=mcfile
-\endverbatim
-(see also \ref COM and \ref PRINT)
+\endplumedfile
In this way, you will be able to use the same masses while processing
a trajectory from the \ref driver . To do so, you need to
@@ -67,11 +66,11 @@ plumed driver --mc mcfile --plumed plumed.dat --ixyz traj.xyz
With the following input you can dump only the charges for a specific
group.
-\verbatim
+\plumedfile
solute_ions: GROUP ATOMS=1-121,200-2012
DUMPATOMS FILE=traj.gro ATOMS=solute_ions STRIDE=100
DUMPMASSCHARGE FILE=mcfile ATOMS=solute_ions
-\endverbatim
+\endplumedfile
Notice however that if you want to process the charges
with the driver (e.g. reading traj.gro) you have to fix atom
numbers first, e.g. with the script
diff --git a/src/generic/DumpProjections.cpp b/src/generic/DumpProjections.cpp
index 3f0d404297be87078fe7e833f8b5efede814cde5..c3a0ca7509104403884c8ca07bcd296681d14507 100644
--- a/src/generic/DumpProjections.cpp
+++ b/src/generic/DumpProjections.cpp
@@ -39,12 +39,12 @@ Dump the derivatives with respect to the input parameters for one or more object
Compute the distance between two groups and write on a file the
derivatives of this distance with respect to all the atoms of the two groups
-\verbatim
+\plumedfile
x1: CENTER ATOMS=1-10
x2: CENTER ATOMS=11-20
d: DISTANCE ATOMS=x1,x2
DUMPPROJECTIONS ARG=d FILE=proj STRIDE=20
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/EffectiveEnergyDrift.cpp b/src/generic/EffectiveEnergyDrift.cpp
index 1c3961390aa08a733668048356ffd9a75809a718..a9ca15e6c8e122d836072fb2924b7f5940b0d50c 100644
--- a/src/generic/EffectiveEnergyDrift.cpp
+++ b/src/generic/EffectiveEnergyDrift.cpp
@@ -55,18 +55,18 @@ Print the effective energy drift described in Ref \cite Ferrarotti2015
This is to monitor the effective energy drift for a metadynamics
simulation on the Debye-Huckel energy. Since this variable is very expensive,
it could be conveniently computed every second step.
-\verbatim
+\plumedfile
dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0
METAD ARG=dh HEIGHT=0.5 SIGMA=0.1 PACE=500 STRIDE=2
EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff
-\endverbatim
+\endplumedfile
This is to monitor if a restraint is too stiff
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=10,20
RESTRAINT ARG=d KAPPA=100000 AT=0.6
EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/FitToTemplate.cpp b/src/generic/FitToTemplate.cpp
index 37e38333f64e5190b6f5b658a27ed920d93a4737..d4bec950191367245208163e2f9a2e4e4e22d32a 100644
--- a/src/generic/FitToTemplate.cpp
+++ b/src/generic/FitToTemplate.cpp
@@ -48,8 +48,9 @@ namespace generic {
This action is used to align a molecule to a template.
This can be used to move the coordinates stored in plumed
-so as to be aligned with a provided template in pdb format. Pdb should contain
-also weights for alignment (see the format of pdb files used e.g. for \ref RMSD).
+so as to be aligned with a provided template in PDB format. Pdb should contain
+also weights for alignment (see the format of PDB files used e.g. for \ref RMSD).
+Make sure your PDB file is correclty formatted as explained \ref pdbreader "in this page".
Weights for displacement are ignored, since no displacement is computed here.
Notice that all atoms (not only those in the template) are aligned.
To see what effect try
@@ -78,13 +79,12 @@ this action is performed at every MD step.
\par Examples
Align the atomic position to a template then print them
-\verbatim
+\plumedfile
# to see the effect, one could dump the atoms before alignment
DUMPATOMS FILE=dump-before.xyz ATOMS=1-20
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE
DUMPATOMS FILE=dump-after.xyz ATOMS=1-20
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
diff --git a/src/generic/Flush.cpp b/src/generic/Flush.cpp
index 78c00f87d5bbaf0169c36eaa3ca6e0f2ac6f26cd..71e9a06d3e144e991373ce501fa3d450205caec4 100644
--- a/src/generic/Flush.cpp
+++ b/src/generic/Flush.cpp
@@ -41,7 +41,7 @@ plumed input file, it will flush all the open files.
\par Examples
A command like this in the input will instruct plumed to flush all the output files every 100 steps
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,10
PRINT ARG=d1 STRIDE=5 FILE=colvar1
@@ -50,7 +50,7 @@ FLUSH STRIDE=100
d2: DISTANCE ATOMS=2,11
# also this print is flushed every 100 steps:
PRINT ARG=d2 STRIDE=10 FILE=colvar2
-\endverbatim
+\endplumedfile
(see also \ref DISTANCE and \ref PRINT).
*/
//+ENDPLUMEDOC
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index 80393a9ce3924e73438f19113cb0212058a2842d..234a01c2828dd8b3ad55c90a225b1dd87e06d363 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -39,21 +39,21 @@ namespace generic {
Define a group of atoms so that a particular list of atoms can be referenced with a single label
in definitions of CVs or virtual atoms.
-Atoms can be listed as comma separated numbers (i.e. 1,2,3,10,45,7,9,..) , simple positive ranges
-(i.e. 20-40), ranges with a stride either positive or negative (i.e. 20-40:2 or 80-50:-2) or as
-combinations of all the former methods (1,2,4,5,10-20,21-40:2,80-50:-2).
+Atoms can be listed as comma separated numbers (i.e. `1,2,3,10,45,7,9`) , simple positive ranges
+(i.e. `20-40`), ranges with a stride either positive or negative (i.e. `20-40:2` or `80-50:-2`) or as
+comma separated combinations of all the former methods (`1,2,4,5,10-20,21-40:2,80-50:-2`).
-Moreover, lists can be imported from ndx files (GROMACS format). Use NDX_FILE to set the name of
-the index file and NDX_GROUP to set the name of the group to be imported (default is first one).
+Moreover, lists can be imported from ndx files (GROMACS format). Use `NDX_FILE` to set the name of
+the index file and `NDX_GROUP` to set the name of the group to be imported (default is first one).
-It is also possible to remove atoms from a list and or sort them using keywords REMOVE, SORT, and UNIQUE.
+It is also possible to remove atoms from a list and or sort them using keywords `REMOVE`, `SORT`, and `UNIQUE`.
The flow is the following:
-- If ATOMS is present take the ordered list of atoms from the ATOMS keyword.
-- If NDX_FILE is present append the list from the the gromacs group.
-- If REMOVE is present remove the first occurence of each of these atoms from the list.
+- If `ATOMS` is present take the ordered list of atoms from the `ATOMS` keyword.
+- If `NDX_FILE` is present append the list from the the gromacs group.
+- If `REMOVE` is present remove the first occurence of each of these atoms from the list.
If one tries to remove an atom that was not listed plumed adds a notice in the output.
-- If SORT is present resulting list is sorted.
-- If UNIQUE is present the resuling list is sorted and duplicate elements are removed.
+- If `SORT` is present resulting list is sorted.
+- If `UNIQUE` is present the resuling list is sorted and duplicate elements are removed.
Notice that this command just creates a shortcut, and does not imply any real calculation.
So, having a huge group defined does not slow down your calculation in any way.
@@ -63,9 +63,9 @@ the \ref INCLUDE command so as to store long group definitions in a separate fil
\par Examples
-This command create a group of atoms containing atoms 1,4,7,11 and 14 (labeled 'o'), and another containing
-atoms 2,3,5,6,8,9,12,13 (labeled 'h'):
-\verbatim
+This command create a group of atoms containing atoms 1, 4, 7, 11 and 14 (labeled 'o'), and another containing
+atoms 2, 3, 5, 6, 8, 9, 12, and 13 (labeled 'h'):
+\plumedfile
o: GROUP ATOMS=1,4,7,11,14
h: GROUP ATOMS=2,3,5,6,8,9,12,13
# compute the coordination among the two groups
@@ -75,45 +75,43 @@ c: COORDINATION GROUPA=o GROUPB=h R_0=0.3
# print the coordination on file 'colvar'
PRINT ARG=c FILE=colvar
-\endverbatim
-(see also \ref COORDINATION and \ref PRINT)
+\endplumedfile
Groups can be conveniently stored in a separate file.
-E.g. one could create a file named 'groups.dat' which reads
-\verbatim
+E.g. one could create a file named `groups.dat` which reads
+\plumedfile
o: GROUP ATOMS=1,4,7,11,14
h: GROUP ATOMS=2,3,5,6,8,9,12,13
-\endverbatim
+\endplumedfile
and then include it in the main 'plumed.dat' file
-\verbatim
+\plumedfile
INCLUDE FILE=groups.dat
# compute the coordination among the two groups
c: COORDINATION GROUPA=o GROUPB=h R_0=0.3
# print the coordination on file 'colvar'
PRINT ARG=c FILE=colvar
-\endverbatim
-(see also \ref INCLUDE, \ref COORDINATION, and \ref PRINT).
-The groups.dat file could be very long and include lists of thousand atoms without cluttering the main plumed.dat file.
+\endplumedfile
+The `groups.dat` file could be very long and include lists of thousand atoms without cluttering the main plumed.dat file.
A GROMACS index file can also be imported
-\verbatim
+\plumedfile
# import group named 'protein' from file index.ndx
pro: GROUP NDX_FILE=index.ndx NDX_GROUP=protein
# dump all the atoms of the protein on a trajectory file
DUMPATOMS ATOMS=pro FILE=traj.gro
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
-A list can be edited with REMOVE
-\verbatim
-# take one atom every three
+A list can be edited with `REMOVE`. For instance, if you
+are using a water model with three atoms per molecule, you can
+easily construct the list of hydrogens in this manner
+\plumedfile
+# take one atom every three, that is oxygens
ox: GROUP ATOMS=1-90:3
-# take the remaining atoms
+# take the remaining atoms, that is hydrogens
hy: GROUP ATOMS=1-90 REMOVE=ox
DUMPATOMS ATOMS=ox FILE=ox.gro
DUMPATOMS ATOMS=hy FILE=hy.gro
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
*/
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index 664c84ba67407f6f44055137f645a09b072940c4..30539f0bb05b5529a60dac5af9e219ad63e31a76 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -38,25 +38,25 @@ Useful to split very large plumed.dat files.
\par Examples
This input
-\verbatim
+\plumedfile
c1: COM ATOMS=1-100
c2: COM ATOMS=101-202
d: DISTANCE ARG=c1,c2
PRINT ARG=d
-\endverbatim
+\endplumedfile
can be replaced with
-\verbatim
+\plumedfile
INCLUDE FILE=pippo.dat
d: DISTANCE ARG=c1,c2
PRINT ARG=d
-\endverbatim
+\endplumedfile
where the content of file pippo.dat is
-\verbatim
+\plumedfile
c1: COM ATOMS=1-100
c2: COM ATOMS=101-202
-\endverbatim
+\endplumedfile
(see also \ref COM, \ref DISTANCE, and \ref PRINT).
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index 2a87d1f7bacef394bb5b5407db01311f8dfdfd2c..74245cf99a3c7ffc2437d2369d6486019e9e68a9 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -40,13 +40,12 @@ to different files. You can control the buffering of output using the \subpage
The following input instructs plumed to print the distance between atoms 3 and 5 on a file
called COLVAR every 10 steps, and the distance and total energy on a file called COLVAR_ALL
every 1000 steps.
-\verbatim
+\plumedfile
DISTANCE ATOMS=2,5 LABEL=distance
ENERGY LABEL=energy
PRINT ARG=distance STRIDE=10 FILE=COLVAR
PRINT ARG=distance,energy STRIDE=1000 FILE=COLVAR_ALL
-\endverbatim
-(See also \ref DISTANCE and \ref ENERGY).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/RandomExchanges.cpp b/src/generic/RandomExchanges.cpp
index be36873bccf097a317e99aaf1270792240a7c319..60d2071207366b50bd2b883df290f33b0172e7ba 100644
--- a/src/generic/RandomExchanges.cpp
+++ b/src/generic/RandomExchanges.cpp
@@ -44,25 +44,25 @@ metadynamics simulation using a different angle in each replica.
Exchanges will be randomly tried between replicas 0-1, 0-2 and 1-2
Here is plumed.0.dat
-\verbatim
+\plumedfile
RANDOM_EXCHANGES
t: TORSION ATOMS=1,2,3,4
METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3
-\endverbatim
+\endplumedfile
Here is plumed.1.dat
-\verbatim
+\plumedfile
RANDOM_EXCHANGES
t: TORSION ATOMS=2,3,4,5
METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3
-\endverbatim
+\endplumedfile
Here is plumed.2.dat
-\verbatim
+\plumedfile
RANDOM_EXCHANGES
t: TORSION ATOMS=3,4,5,6
METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3
-\endverbatim
+\endplumedfile
\warning Multi replica simulations are presently only working with gromacs.
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index 88c279630021b47e6fd1e3e3ea4aa904e161ac69..63b8f8fc801157b83b460b1f0010bf777002c8d8 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -52,11 +52,11 @@ This input reads in data from a file called input_colvar.data that was generated
in a calculation that involved PLUMED. The first command reads in the data from the
column headed phi1 while the second reads in the data from the column headed phi2.
-\verbatim
+\plumedfile
rphi1: READ FILE=input_colvar.data VALUES=phi1
rphi2: READ FILE=input_colvar.data VALUES=phi2
PRINT ARG=rphi1,rphi2 STRIDE=500 FILE=output_colvar.data
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/ResetCell.cpp b/src/generic/ResetCell.cpp
index fd14c1fe102f5a873c6ce5d4623df4e0b2b94100..5268d52de348b3271e0b076a072c32d480d09e69 100644
--- a/src/generic/ResetCell.cpp
+++ b/src/generic/ResetCell.cpp
@@ -71,14 +71,13 @@ this action is performed at every MD step.
\par Examples
Reset cell to be triangular after a rototranslational fit
-\verbatim
+\plumedfile
DUMPATOMS FILE=dump-original.xyz ATOMS=1-20
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=OPTIMAL
DUMPATOMS FILE=dump-fit.xyz ATOMS=1-20
RESET_CELL TYPE=TRIANGULAR
DUMPATOMS FILE=dump-reset.xyz ATOMS=1-20
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
*/
diff --git a/src/generic/Time.cpp b/src/generic/Time.cpp
index 3512cb53da5c7f1a1fac71517c3712a8b16aa115..9a821f0b65dcf0a1318d6bb19ed5f005527f340a 100644
--- a/src/generic/Time.cpp
+++ b/src/generic/Time.cpp
@@ -35,11 +35,10 @@ retrieve the time of the simulation to be used elsewere
\par Examples
-\verbatim
+\plumedfile
TIME LABEL=t1
PRINT ARG=t1
-\endverbatim
-(See also \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/UpdateIf.cpp b/src/generic/UpdateIf.cpp
index 2d067fcf3db179ca6ce259b41a611dfd262908fc..696e66c20f4eb423b661ba3214fcf2b68ca8953e 100644
--- a/src/generic/UpdateIf.cpp
+++ b/src/generic/UpdateIf.cpp
@@ -62,7 +62,7 @@ can lead to unexpected results.
\par Examples
The following input instructs plumed dump all the snapshots where an atom is in touch with
the solute.
-\verbatim
+\plumedfile
solute: GROUP ATOMS=1-124
coord: COORDINATION GROUPA=solute GROUPB=500 R_0=0.5
@@ -72,8 +72,7 @@ coord: COORDINATION GROUPA=solute GROUPB=500 R_0=0.5
UPDATE_IF ARG=coord MORE_THAN=0.5
DUMPATOMS ATOMS=solute,500 FILE=output.xyz
UPDATE_IF ARG=coord END
-\endverbatim
-(See also \ref GROUP, \ref COORDINATION, and \ref DUMPATOMS)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp
index 12e9c82813bb10b53540f9598ff4a0304b9adb8d..e43c0aa07b571e2dfa9498146b5f2f4b24dfe7e3 100644
--- a/src/generic/WholeMolecules.cpp
+++ b/src/generic/WholeMolecules.cpp
@@ -74,30 +74,27 @@ to skip some atoms, provided consecute chosen atoms are close enough.
This command instructs plumed to reconstruct the molecule containing atoms 1-20
at every step of the calculation and dump them on a file.
-\verbatim
+\plumedfile
# to see the effect, one could dump the atoms as they were before molecule reconstruction:
# DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20
WHOLEMOLECULES ENTITY0=1-20
DUMPATOMS FILE=dump.xyz ATOMS=1-20
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
This command instructs plumed to reconstruct two molecules containing atoms 1-20 and 30-40
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-20 ENTITY1=30-40
DUMPATOMS FILE=dump.xyz ATOMS=1-20,30-40
-\endverbatim
-(see also \ref DUMPATOMS)
+\endplumedfile
This command instructs plumed to reconstruct the chain of backbone atoms in a
protein
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES RESIDUES=all MOLTYPE=protein
-\endverbatim
-(See also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/WrapAround.cpp b/src/generic/WrapAround.cpp
index 946a060fdef55569d473b09559adf427d4da969b..6320ee4bbca6434e9dad48ffdf0a2ac2d9226dcb 100644
--- a/src/generic/WrapAround.cpp
+++ b/src/generic/WrapAround.cpp
@@ -69,20 +69,19 @@ consider the possibility of using the STRIDE keyword here (with great care).
This command instructs plumed to move all the ions to their periodic image that is as close as possible to
the rna group.
-\verbatim
+\plumedfile
rna: GROUP ATOMS=1-100
ions: GROUP ATOMS=101-110
# first make the rna molecule whole
WHOLEMOLECULES ENTITY0=rna
WRAPAROUND ATOMS=ions AROUND=rna
DUMPATOMS FILE=dump.xyz ATOMS=rna,ions
-\endverbatim
-(see also \ref WHOLEMOLECULES, \ref GROUP and \ref DUMPATOMS)
+\endplumedfile
In case you want to do it during a simulation and you only care about wrapping the ions in
the `dump.xyz` file, you can use the following:
-\verbatim
+\plumedfile
# add some restraint that do not require molecules to be whole:
a: TORSION ATOMS=1,2,10,11
RESTRAINT ARG=a AT=0.0 KAPPA=5
@@ -98,15 +97,14 @@ ions: GROUP ATOMS=101-110
WHOLEMOLECULES ENTITY0=rna STRIDE=100
WRAPAROUND ATOMS=ions AROUND=rna STRIDE=100
DUMPATOMS FILE=dump.xyz ATOMS=rna,ions STRIDE=100
-\endverbatim
-(see also \ref TORSION, \ref GROUP, \ref WHOLEMOLECULES and \ref DUMPATOMS)
+\endplumedfile
Notice that if the biased variable requires a molecule to be whole, you might have to put
just the \ref WHOLEMOLECULES command before computing that variable and leave the default STRIDE=1.
This command instructs plumed to center all atoms around the center of mass of a solute molecule.
-\verbatim
+\plumedfile
solute: GROUP ATOMS=1-100
all: GROUP ATOMS=1-1000
# center of the solute:
@@ -116,8 +114,7 @@ com: COM ATOMS=solute
# notice that we wrap around a single atom. this should be fast
WRAPAROUND ATOMS=all AROUND=com
DUMPATOMS FILE=dump.xyz ATOMS=all
-\endverbatim
-(see also \ref GROUP \ref COM \ref DUMPATOMS)
+\endplumedfile
Notice that whereas \ref WHOLEMOLECULES is designed to make molecules whole,
\ref WRAPAROUND can easily break molecules. In the last example,
@@ -136,7 +133,7 @@ in the following examples all the water oxygens will be brought
close to the solute, and all the hydrogens will be kept close
to their related oxygen.
-\verbatim
+\plumedfile
solute: GROUP ATOMS=1-100
water: GROUP ATOMS=101-1000
com: COM ATOMS=solute
@@ -145,8 +142,7 @@ WRAPAROUND ATOMS=solute AROUND=com
# notice that we wrap around a single atom. this should be fast
WRAPAROUND ATOMS=water AROUND=com GROUPBY=3
DUMPATOMS FILE=dump.xyz ATOMS=solute,water
-\endverbatim
-(see also \ref GROUP \ref COM \ref DUMPATOMS)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/ConvertToFES.cpp b/src/gridtools/ConvertToFES.cpp
index 4e3bbdf1705a63638b0ef08c1fe6658eda4b304a..661aa2bde96e2116adb664bc58c5156d97d0923c 100644
--- a/src/gridtools/ConvertToFES.cpp
+++ b/src/gridtools/ConvertToFES.cpp
@@ -46,12 +46,12 @@ and the HISTOGRAM action. All the data within this trajectory is used in the co
HISTOGRAM. Finally, once all the data has been read in, the histogram is converted to a free energy
using the formula above and the free energy is output to a file called fes.dat
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
ff: CONVERT_TO_FES GRID=hA1 TEMP=300
DUMPGRID GRID=ff FILE=fes.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/DumpCube.cpp b/src/gridtools/DumpCube.cpp
index 0fbc47f566575199de0688a5277fb391d96efcb2..f1df7406e75d598937d67bd313b0bdfcd3715ce4 100644
--- a/src/gridtools/DumpCube.cpp
+++ b/src/gridtools/DumpCube.cpp
@@ -46,14 +46,14 @@ between atoms 1 and 2, the distance between atom 1 and 3 and the angle between t
all the kernels have been added the resulting histogram is output to a file called histoA1.cube. This file has the
Gaussian cube file format. The histogram can thus be visualized using tools such as VMD.
-\verbatim
+\plumedfile
x1: DISTANCE ATOMS=1,2
x2: DISTANCE ATOMS=1,3
x3: ANGLE ATOMS=1,2,3
hA1: HISTOGRAM ARG=x1,x2,x3 GRID_MIN=0.0,0.0,0.0 GRID_MAX=3.0,3.0,3.0 GRID_BIN=10,10,10 BANDWIDTH=1.0,1.0,1.0
DUMPCUBE GRID=hA1 FILE=histoA1.cube
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/DumpGrid.cpp b/src/gridtools/DumpGrid.cpp
index 608742a8bfb48a1b9395b7906ac21363c42aa4e1..e3524d563d67aa96c091fb389984959385c6a9de 100644
--- a/src/gridtools/DumpGrid.cpp
+++ b/src/gridtools/DumpGrid.cpp
@@ -67,7 +67,7 @@ for y. This block is then followed by a blank line again and this pattern conti
The following input monitors two torsional angles during a simulation
and outputs a continuos histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -80,11 +80,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a discrete histogram as a function of them at the end of the simulation.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -98,11 +98,11 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs the histogram accumulated thus far every 100000 steps.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -115,14 +115,14 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
The following input monitors two torsional angles during a simulation
and outputs a separate histogram for each 100000 steps worth of trajectory.
Notice how the CLEAR keyword is used here and how it is not used in the
previous example.
-\verbatim
+\plumedfile
TORSION ATOMS=1,2,3,4 LABEL=r1
TORSION ATOMS=2,3,4,5 LABEL=r2
HISTOGRAM ...
@@ -136,7 +136,7 @@ HISTOGRAM ...
... HISTOGRAM
DUMPGRID GRID=hh FILE=histo STRIDE=100000
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/FindContour.cpp b/src/gridtools/FindContour.cpp
index a58e4f650e4dddf7a05733ae729cb9d77ab700f5..1bae86d431cce76f9d7b98b24420bdcec41292b2 100644
--- a/src/gridtools/FindContour.cpp
+++ b/src/gridtools/FindContour.cpp
@@ -67,7 +67,7 @@ solidness at each point in the simulation cell. The Willard-Chandler dividing s
at which the value of this phase field is equal to 0.5. This set of points is output to file called mycontour.dat. A new contour
is found on every single step for each frame that is read in.
-\verbatim
+\plumedfile
UNITS NATURAL
FCCUBIC ...
SPECIES=1-96000 SWITCH={CUBIC D_0=1.2 D_MAX=1.5}
@@ -84,7 +84,7 @@ MULTICOLVARDENS ...
... MULTICOLVARDENS
FIND_CONTOUR GRID=dens CONTOUR=0.5 FILE=mycontour.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/FindSphericalContour.cpp b/src/gridtools/FindSphericalContour.cpp
index a2ee2aa8627c0a1fb231f79111d936d5e5e25ffe..7d36e818c882e99fcba0085a6409093cf8d7b425 100644
--- a/src/gridtools/FindSphericalContour.cpp
+++ b/src/gridtools/FindSphericalContour.cpp
@@ -81,7 +81,7 @@ by exploiting the functionality within \ref CENTER_OF_MULTICOLVAR. We can then
cluster and the values of the coordination numbers of these atoms. The final line in the input then finds the a set of points on the dividing surface that separates
teh droplet from the surrounding gas. The value of the phase field on this isocontour is equal to 0.75.
-\verbatim
+\plumedfile
# Calculate coordination numbers
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
# Select coordination numbers that are more than 2.0
@@ -98,7 +98,7 @@ cent: CENTER_OF_MULTICOLVAR DATA=trans1
dens: MULTICOLVARDENS DATA=trans1 ORIGIN=cent DIR=xyz NBINS=30,30,30 BANDWIDTH=2.0,2.0,2.0
# Find the isocontour around the nucleus
FIND_SPHERICAL_CONTOUR GRID=dens CONTOUR=0.85 INNER_RADIUS=10.0 OUTER_RADIUS=40.0 FILE=mysurface.xyz UNITS=A PRECISION=4 NPOINTS=100
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/FourierTransform.cpp b/src/gridtools/FourierTransform.cpp
index 5a53b390dec72635b5c802995b12635942260a58..87a078336ebc5f7a4dfd2d7a8426a16d4be91386 100644
--- a/src/gridtools/FourierTransform.cpp
+++ b/src/gridtools/FourierTransform.cpp
@@ -57,9 +57,9 @@ The default values of these parameters are: \f$a=1\f$ and \f$b=1\f$.
\par Examples
The following example tells Plumed to compute the complex 2D 'backward' Discrete Fourier Transform by taking the data saved on a grid called 'density', and normalizing the output by \f$ \frac{1}{\sqrt{N_x\, N_y}}\f$, where \f$N_x\f$ and \f$N_y\f$ are the number of data on the grid (it can be the case that \f$N_x \neq N_y\f$):
-\verbatim
+\plumedfile
FOURIER_TRANSFORM STRIDE=1 GRID=density FT_TYPE=complex FOURIER_PARAMETERS=0,-1 FILE=fourier.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/InterpolateGrid.cpp b/src/gridtools/InterpolateGrid.cpp
index e8f97c0d4abe25e86dff08372a69e63bdc5b62cd..7fbc1d65d334757ce8e712cc59345f6202eb878f 100644
--- a/src/gridtools/InterpolateGrid.cpp
+++ b/src/gridtools/InterpolateGrid.cpp
@@ -38,12 +38,12 @@ distance between atoms 1 and 2 using kernel density estimation. During the calc
are evaluated at 100 points on a uniform grid between 0.0 and 3.0. Prior to outputting this function at the end of the
simulation this function is interpolated onto a finer grid of 200 points between 0.0 and 3.0.
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1
ii: INTERPOLATE_GRID GRID=hA1 GRID_BIN=200
DUMPGRID GRID=ii FILE=histo.dat
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/maketools/plumedcheck b/src/maketools/plumedcheck
index 120808decbabe905049f6c393a0cfbf14e68cfa3..5886ec086329d18d12c27278b206160a4c6c2869 100755
--- a/src/maketools/plumedcheck
+++ b/src/maketools/plumedcheck
@@ -354,6 +354,12 @@ BEGINFILE{
if(in_plumed_doc && (in_plumed_doc in provide_examples) && match($0,"^ *\\\\verbatim *$")){
provide_verbatim[in_plumed_doc]=1
}
+# check if, besides the \par Examples text, there is a plumedfile command
+# now it is considered equivalent to a verbatim
+# later on we might make plumedfile compulsory instead of verbatim
+ if(in_plumed_doc && (in_plumed_doc in provide_examples) && match($0,"^ *\\\\plumedfile *$")){
+ provide_verbatim[in_plumed_doc]=1
+ }
#print match($0,"^ *\\\\verbatim *$"),"X" $0 "X"
# take note of actions or cltools that provide examples
diff --git a/src/manyrestraints/LWalls.cpp b/src/manyrestraints/LWalls.cpp
index 7c0ad569ecb1ba59a48b18616bae7292086ab711..c98405d04e40d3a232d052f43ac38f3df99662c3 100644
--- a/src/manyrestraints/LWalls.cpp
+++ b/src/manyrestraints/LWalls.cpp
@@ -45,10 +45,10 @@ The following set of commands can be used to stop any of the 800 atoms in group
in the z direction from atom 34137. This is done by adding a lower wall on the z-distance between all the atoms in
group A and the position of 34137.
-\verbatim
+\plumedfile
l: ZDISTANCES GROUPA=1-800 GROUPB=34137 NOPBC
LWALLS DATA=l AT=2.46465 KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=lwall
-\endverbatim
+\endplumedfile
*/
diff --git a/src/manyrestraints/UWalls.cpp b/src/manyrestraints/UWalls.cpp
index f4c75f0d8976ac05aed11169d607fe16040c9b76..2c0f75367da490b1cba34e54896379e47a4eddd5 100644
--- a/src/manyrestraints/UWalls.cpp
+++ b/src/manyrestraints/UWalls.cpp
@@ -48,11 +48,11 @@ and the center of mass of the cluster. These distances are then passed to the U
a \ref UPPER_WALLS restraint on each of them and thereby prevents each of them from moving very far from the centre
of mass of the cluster.
-\verbatim
+\plumedfile
COM ATOMS=1-20 LABEL=c1
DISTANCES GROUPA=c1 GROUPB=1-20 LABEL=d1
UWALLS DATA=d1 AT=2.5 KAPPA=0.2 LABEL=sr
-\endverbatim
+\endplumedfile
*/
diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index d029720ed843f89007cb6e344684bcd1ab06b1ec..20ae003016ae482155fc3d8ee446e8a7813fb829 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -76,10 +76,10 @@ frame are removed from these displacements. The matrix \f$A\f$ and the referenc
configuration \f$R^{ref}\f$ are specified in the pdb input file reference.pdb and the
value of all projections (and the residual) are output to a file called colvar2.
-\verbatim
+\plumedfile
PCAVARS REFERENCE=reference.pdb TYPE=OPTIMAL LABEL=pca2
PRINT ARG=pca2.* FILE=colvar2
-\endverbatim
+\endplumedfile
The reference configurations can be specified using a pdb file. The first configuration that you provide is the reference configuration,
which is refered to in the above as \f$X^{ref}\f$ subsequent configurations give the directions of row vectors that are contained in
diff --git a/src/mapping/Path.cpp b/src/mapping/Path.cpp
index 37db777d2e1677f2fa75198affee22c484dbd8e8..4808fad15dd52176845faa3afea24d097c0caad0 100644
--- a/src/mapping/Path.cpp
+++ b/src/mapping/Path.cpp
@@ -73,21 +73,21 @@ In the example below the path is defined using RMSD distance from frames.
The reference frames in the path are defined in the pdb file. In this frame
each configuration in the path is separated by a line containing just the word END.
-\verbatim
+\plumedfile
p1: PATH REFERENCE=file.pdb TYPE=OPTIMAL LAMBDA=500.0
PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
In the example below the path is defined using the values of two torsional angles (t1 and t2).
In addition, the \f$s\f$ and \f$z\f$ are calculated using the geometric expressions described
above rather than the alegebraic expressions that are used by default.
-\verbatim
+\plumedfile
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
pp: PATH TYPE=EUCLIDEAN REFERENCE=epath.pdb GPATH NOSPATH NOZPATH
PRINT ARG=pp.* FILE=colvar
-\endverbatim
+\endplumedfile
Notice that the LAMBDA parameter is not required here as we are not calculating \f$s\f$ and \f$s\f$
using the algebraic formulae defined earlier. The positions of the frames in the path are defined
@@ -109,19 +109,19 @@ The following input instructs PLUMED to calculate the values of the path collect
path are defined in the file all.pdb and all distances are measured using the OPTIMAL metric that is discussed in the manual
page on \ref RMSD.
-\verbatim
+\plumedfile
p2: PATH REFERENCE=all.pdb LAMBDA=69087
PRINT ARG=p2.spath,p2.zpath STRIDE=1 FILE=colvar
-\endverbatim
+\endplumedfile
If you wish to use collective variable values in the definition of your path you would use an input file with something like this:
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=3,4a
p2: PATH REFERENCE=mypath.pdb LAMBDA=2 TYPE=EUCLIDEAN
PRINT ARG=p2.spath,p2.zpath STRIDE=1 FILE=colvar
-\endverbatim
+\endplumedfile
The corresponding pdb file containing the definitions of the frames in the path would then look like this:
diff --git a/src/mapping/PropertyMap.cpp b/src/mapping/PropertyMap.cpp
index 9da32b47bbad984703c06559560ec992115d27a5..91c96f4dd650734700561adadb19a868b2fd1ce1 100644
--- a/src/mapping/PropertyMap.cpp
+++ b/src/mapping/PropertyMap.cpp
@@ -47,10 +47,10 @@ that these properties take at a set of reference configurations and using the fo
between the reference configurations and the instantaneous configurations are calculated using the OPTIMAL metric that is
discussed at length in the manual pages on \ref RMSD.
-\verbatim
+\plumedfile
p2: GPROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087
PRINT ARG=p2.X,p2.Y,p2.zpath STRIDE=1 FILE=colvar
-\endverbatim
+\endplumedfile
The additional input file for this calculation, which contains the reference frames and the values of X and Y at these reference
points has the following format.
diff --git a/src/multicolvar/AlphaBeta.cpp b/src/multicolvar/AlphaBeta.cpp
index 01379c58374c04184de72ee675fef4c8b338b2d5..aea79fc2ea288a922e5897281e718f759902cfc1 100644
--- a/src/multicolvar/AlphaBeta.cpp
+++ b/src/multicolvar/AlphaBeta.cpp
@@ -49,7 +49,7 @@ The \f$\phi_i^{\textrm{Ref}}\f$ values are the user-specified reference values f
The following provides an example of the input for an alpha beta similarity.
-\verbatim
+\plumedfile
ALPHABETA ...
ATOMS1=168,170,172,188 REFERENCE1=3.14
ATOMS2=170,172,188,190 REFERENCE2=3.14
@@ -57,11 +57,11 @@ ATOMS3=188,190,192,230 REFERENCE3=3.14
LABEL=ab
... ALPHABETA
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Because all the reference values are the same we can calculate the same quantity using
-\verbatim
+\plumedfile
ALPHABETA ...
ATOMS1=168,170,172,188 REFERENCE=3.14
ATOMS2=170,172,188,190
@@ -69,13 +69,13 @@ ATOMS3=188,190,192,230
LABEL=ab
... ALPHABETA
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you
can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
ALPHABETA ...
ATOMS1=@phi-3 REFERENCE=3.14
@@ -84,7 +84,7 @@ ATOMS3=@phi-4
LABEL=ab
... ALPHABETA
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/multicolvar/Angles.cpp b/src/multicolvar/Angles.cpp
index a42233cbd4de4fbdfef9942dc4aa674e6522256d..cdc062579991198e890a2aeed8675dd69cf33ebc 100644
--- a/src/multicolvar/Angles.cpp
+++ b/src/multicolvar/Angles.cpp
@@ -58,28 +58,28 @@ an atom / molecule \cite lj-recon.
The following example instructs plumed to find the average of two angles and to
print it to a file
-\verbatim
+\plumedfile
ANGLES ATOMS1=1,2,3 ATOMS2=4,5,6 MEAN LABEL=a1
PRINT ARG=a1.mean FILE=colvar
-\endverbatim
+\endplumedfile
The following example tells plumed to calculate all angles involving
at least one atom from GROUPA and two atoms from GROUPB in which the distances
are less than 1.0. The number of angles between \f$\frac{\pi}{4}\f$ and
\f$\frac{3\pi}{4}\f$ is then output
-\verbatim
+\plumedfile
ANGLES GROUPA=1-10 GROUPB=11-100 BETWEEN={GAUSSIAN LOWER=0.25pi UPPER=0.75pi} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1
PRINT ARG=a1.between FILE=colvar
-\endverbatim
+\endplumedfile
This final example instructs plumed to calculate all the angles in the first coordination
spheres of the atoms. A discretized-normalized histogram of the distribution is then output
-\verbatim
+\plumedfile
ANGLES GROUP=1-38 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=pi NBINS=20} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1
PRINT ARG=a1.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Bridge.cpp b/src/multicolvar/Bridge.cpp
index 42198ffa1e26ddebc91b2a840dd0a40f92c22a22..53e76158b5f6339f3da4b666ff2bdfaba340ec91 100644
--- a/src/multicolvar/Bridge.cpp
+++ b/src/multicolvar/Bridge.cpp
@@ -51,10 +51,10 @@ The following example instructs plumed to calculate the number of water molecule
that are bridging betweeen atoms 1-10 and atoms 11-20 and to print the value
to a file
-\verbatim
+\plumedfile
BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 LABEL=w1
PRINT ARG=a1.mean FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/CenterOfMultiColvar.cpp b/src/multicolvar/CenterOfMultiColvar.cpp
index f8b5be66001a8defaef7b40d443d8d667ce2d7fe..0708bd4025863b288082bb56e17cee3a6e39bd83 100644
--- a/src/multicolvar/CenterOfMultiColvar.cpp
+++ b/src/multicolvar/CenterOfMultiColvar.cpp
@@ -55,10 +55,10 @@ As you want to calculate the position of the droplets you thus recognise that th
numbers should have a high weight in the weighted average you are using to calculate the position of the droplet.
You can thus calculate the position of the droplet using an input like the one shown below:
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
cc: CENTER_OF_MULTICOLVAR DATA=c1
-\endverbatim
+\endplumedfile
The first line here calclates the coordination numbers of all the atoms in the system. The virtual atom then uses the values
of the coordination numbers calculated by the action labelled c1 when it calculates the Berry Phase average described above.
@@ -66,11 +66,11 @@ of the coordination numbers calculated by the action labelled c1 when it calcula
The above input is fine we can, however, refine this somewhat by making use of a multicolvar transform action as shown below:
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
cf: MTRANSFORM_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
cc: CENTER_OF_MULTICOLVAR DATA=cf
-\endverbatim
+\endplumedfile
This input once again calculates the coordination numbers of all the atoms in the system. The middle line then transforms these
coordinations numbers to numbers between 0 and 1. Essentially any atom with a coordination number larger than 2.0 is given a weight
diff --git a/src/multicolvar/CoordinationNumbers.cpp b/src/multicolvar/CoordinationNumbers.cpp
index a3823b4887d687ed220cb85eee20efa29fed304b..38c26d348b9486b9c000c68e261a6395af081b3c 100644
--- a/src/multicolvar/CoordinationNumbers.cpp
+++ b/src/multicolvar/CoordinationNumbers.cpp
@@ -48,16 +48,16 @@ s = \frac{ 1 - \left(\frac{r-d_0}{r_0}\right)^n } { 1 - \left(\frac{r-d_0}{r_0}\
The following input tells plumed to calculate the coordination numbers of atoms 1-100 with themselves.
The minimum coordination number is then calculated.
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 MIN={BETA=0.1}
-\endverbatim
+\endplumedfile
The following input tells plumed to calculate how many atoms from 1-100 are within 3.0 of each of the atoms
from 101-110. In the first 101 is the central atom, in the second 102 is the central atom and so on. The
number of coordination numbers more than 6 is then computed.
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIESA=101-110 SPECIESB=1-100 R_0=3.0 MORE_THAN={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Density.cpp b/src/multicolvar/Density.cpp
index 0351140a3f309a0f63d4ebdf387c73188761b676..598e16b30929e759fcc4e69d15ef93f7d13da9c6 100644
--- a/src/multicolvar/Density.cpp
+++ b/src/multicolvar/Density.cpp
@@ -40,11 +40,11 @@ the number of atoms in half the box.
The following example calculates the number of atoms in one half of the simulation box.
-\verbatim
+\plumedfile
DENSITY SPECIES=1-100 LABEL=d
AROUND ARG=d XLOWER=0.0 XUPPER=0.5 LABEL=d1
PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
index e75bde668092da07212a91a7aa4641bd7a4f7406..a1f5ea87295680e3a7cd10a76addfefd4944a6da 100644
--- a/src/multicolvar/DihedralCorrelation.cpp
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -48,14 +48,14 @@ where the \f$\phi_i\f$ and \f$\psi\f$ values and the instantaneous values for th
The following provides an example input for the dihcor action
-\verbatim
+\plumedfile
DIHCOR ...
ATOMS1=1,2,3,4,5,6,7,8
ATOMS2=5,6,7,8,9,10,11,12
LABEL=dih
... DIHCOR
PRINT ARG=dih FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
In the above input we are calculating the correation between the torsion angle involving atoms 1, 2, 3 and 4 and the torsion angle
involving atoms 5, 6, 7 and 8. This is then added to the correlation betwene the torsion angle involving atoms 5, 6, 7 and 8 and the
@@ -65,7 +65,7 @@ Writing out the atoms involved in all the torsions in this way can be rather ted
can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
DIHCOR ...
ATOMS1=@phi-3,@psi-3
@@ -73,7 +73,7 @@ ATOMS2=@psi-3,@phi-4
ATOMS4=@phi-4,@psi-4
... DIHCOR
PRINT ARG=dih FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/multicolvar/DistanceFromContour.cpp b/src/multicolvar/DistanceFromContour.cpp
index 214930392e0e2dffaab6c222a02c5043e50172b0..6f99e214a478ff53c3f3c5fea9ed3a059e09cec0 100644
--- a/src/multicolvar/DistanceFromContour.cpp
+++ b/src/multicolvar/DistanceFromContour.cpp
@@ -58,10 +58,10 @@ In this example atoms 2-100 are assumed to be concentraed along some part of the
an interface between a liquid/solid and the vapour. The quantity dc measures the distance between the
surface at which the density of 2-100 atoms is equal to 0.2 and the position of the test particle atom 1.
-\verbatim
+\plumedfile
dens: DENSITY SPECIES=2-100
dc: DISTANCE_FROM_CONTOUR DATA=dens ATOM=1 BANDWIDTH=0.5,0.5,0.5 DIR=z CONTOUR=0.2
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index d5cb8fde0026618b2b4df7c5de24c3c9c38319d9..579668b8807085dc092ac1db6171b4abd2aa00c2 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -42,36 +42,36 @@ distances such as the minimum, the number less than a certain quantity and so on
The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2 and to
print the minimum for these two distances.
-\verbatim
+\plumedfile
DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2
and then to calculate the number of these distances that are less than 0.1 nm. The number of distances
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
DISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate all the distances between atoms 1, 2 and 3 (i.e. the distances between atoms
1 and 2, atoms 1 and 3 and atoms 2 and 3). The average of these distances is then calculated.
-\verbatim
+\plumedfile
DISTANCES GROUP=1-3 MEAN LABEL=d1
PRINT ARG=d1.mean
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the distances between the atoms in GROUPA and the atoms in GROUPB.
In other words the distances between atoms 1 and 2 and the distance between atoms 1 and 3. The number of distances
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
@@ -79,10 +79,10 @@ PRINT ARG=d1.gt0.1
To calculate and print the minimum distance between two groups of atoms you use the following commands
-\verbatim
+\plumedfile
d1: DISTANCES GROUPA=1-10 GROUPB=11-20 MIN={BETA=500.}
PRINT ARG=d1.min FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
(see \ref DISTANCES and \ref PRINT)
In order to ensure differentiability the minimum is calculated using the following function:
@@ -102,7 +102,7 @@ allow you to calculate multiple functions of a distribution of simple collective
can calculate the number of distances less than 1.0, the minimum distance, the number of distances more than
2.0 and the number of distances between 1.0 and 2.0 by using the following command:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LESS_THAN={RATIONAL R_0=1.0}
@@ -111,7 +111,7 @@ DISTANCES ...
MIN={BETA=500.}
... DISTANCES
PRINT ARG=d1.lessthan,d1.morethan,d1.between,d1.min FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
(see \ref DISTANCES and \ref PRINT)
A calculation performed this way is fast because the expensive part of the calculation - the calculation of all the distances - is only
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index 27029a43690b7b658389a5b8bf465b2fe67fed25..fb08af5b4437eb54b8cb6e07d63e2380f13626ef 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -49,13 +49,13 @@ In this examples we calculate the distances between the atoms of the first and
group and we write them in the file MULTICOLVAR.xyz. For each couple it writes the
coordinates of their geometric center and their distance.
-\verbatim
+\plumedfile
pos: GROUP ATOMS=220,221,235,236,247,248,438,439,450,451,534,535
neg: GROUP ATOMS=65,68,138,182,185,267,270,291,313,316,489,583,621,711
DISTANCES GROUPA=pos GROUPB=neg LABEL=slt
DUMPMULTICOLVAR DATA=slt FILE=MULTICOLVAR.xyz
-\endverbatim
+\endplumedfile
(see also \ref DISTANCES)
diff --git a/src/multicolvar/FilterBetween.cpp b/src/multicolvar/FilterBetween.cpp
index d6a4187118d5c3a35407aa466f5b2900ebad281a..17ad0be9e5308560121d3d8ea4e78263c3f49cc2 100644
--- a/src/multicolvar/FilterBetween.cpp
+++ b/src/multicolvar/FilterBetween.cpp
@@ -59,22 +59,22 @@ In other words, you are calculating the mean for the transformed colvar.
The following input gives an example of how a MTRANSFORM_BETWEEN action can be used to duplicate
functionality that is elsehwere in PLUMED.
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LABEL=d1
... DISTANCES
MTRANSFORM_BETWEEN DATA=d1 LOWER=1.0 UPPER=2.0 SMEAR=0.5
-\endverbatim
+\endplumedfile
In this case you can achieve the same result by using:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0}
... DISTANCES
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
The advantage of MTRANSFORM_BETWEEN comes, however, if you want to use transformed colvars as input
@@ -112,10 +112,10 @@ One is thus calculating the mean for those colvars that are within the range of
The example shown below calculates the mean for those distances that are between 0 and 3 nm in length
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1
MFILTER_BETWEEN DATA=d1 LOWER=0 UPPER=3.0 SMEAR=0.0001 MEAN LABEL=d4
-\endverbatim
+\endplumedfile
More complicated things can be done by using the label of a filter as input to a new multicolvar as shown
in the example below. Here the coordination numbers of all atoms are computed. The atoms with a coordination
@@ -123,11 +123,11 @@ number between 4 and 6 are then identified using the filter. This reduced list
to a second coordination number calculation. This second coordination number thus measures the number of atoms
4-6 coordinated atoms each of the 4-6 coordination atoms is bound to.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
cf: MFILTER_BETWEEN DATA=c1 LOWER=4 UPPER=6 SMEAR=0.5 LOWMEM
c2: COORDINATIONNUMBER SPECIES=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} MORE_THAN={RATIONAL D_0=2.0 R_0=0.1}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/FilterLessThan.cpp b/src/multicolvar/FilterLessThan.cpp
index 6363bcbb430b7faf42f6d189d241bf9ff5b820a4..e65d5fcd1872a840a20050ff82521bd8b47199d0 100644
--- a/src/multicolvar/FilterLessThan.cpp
+++ b/src/multicolvar/FilterLessThan.cpp
@@ -51,22 +51,22 @@ In other words, you are calculating the mean for the transformed colvar.
The following input gives an example of how a MTRANSFORM_LESS action can be used to duplicate
functionality that is elsehwere in PLUMED.
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LABEL=d1
... DISTANCES
MTRANSFORM_LESS DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
-\endverbatim
+\endplumedfile
In this case you can achieve the same result by using:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LESS_THAN={GAUSSIAN D_0=1.5 R_0=0.00001}
... DISTANCES
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
The advantage of MTRANSFORM_LESS comes, however, if you want to use transformed colvars as input
@@ -99,10 +99,10 @@ One is thus calculating the mean for those colvars that are less than the target
The example shown below calculates the mean for those distances that less than 1.5 nm in length
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1
MFILTER_LESS DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001} MEAN LABEL=d4
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/FilterMoreThan.cpp b/src/multicolvar/FilterMoreThan.cpp
index 961c33d01627d1205d051c3e0430dd7032a2be33..50c1dc59b5228cfd0dccf01c038f1e07f7da0808 100644
--- a/src/multicolvar/FilterMoreThan.cpp
+++ b/src/multicolvar/FilterMoreThan.cpp
@@ -51,22 +51,22 @@ In other words, you are calculating the mean for the transformed colvar.
The following input gives an example of how a MTRANSFORM_MORE action can be used to duplicate
functionality that is elsehwere in PLUMED.
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LABEL=d1
... DISTANCES
MTRANSFORM_MORE DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
-\endverbatim
+\endplumedfile
In this case you can achieve the same result by using:
-\verbatim
+\plumedfile
DISTANCES ...
GROUPA=1-10 GROUPB=11-20
MORE_THAN={GAUSSIAN D_0=1.5 R_0=0.00001}
... DISTANCES
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
The advantage of MTRANSFORM_MORE comes, however, if you want to use transformed colvars as input
@@ -104,10 +104,10 @@ One is thus calculating the mean for those colvars that are greater than the tar
The example shown below calculates the mean for those distances that greater than 1.5 nm in length
-\verbatim
+\plumedfile
DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1
MFILTER_MORE DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001} MEAN LABEL=d4
-\endverbatim
+\endplumedfile
More complicated things can be done by using the label of a filter as input to a new multicolvar as shown
in the example below. Here the coordination numbers of all atoms are computed. The atoms with a coordination
@@ -115,11 +115,11 @@ number greater than 2 are then identified using the filter. This reduced list o
to a second coordination number calculation. This second coordination number thus measures the number of
two-coordinated atoms that each of the two-coordinated atoms is bound to.
-\verbatim
+\plumedfile
1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
c2: COORDINATIONNUMBER SPECIES=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} MORE_THAN={RATIONAL D_0=2.0 R_0=0.1}
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/InPlaneDistances.cpp b/src/multicolvar/InPlaneDistances.cpp
index d041fa1e0248477f15a1850e401b37115f116152..ef9f4a55f52d68932aec143af01146c508050e2f 100644
--- a/src/multicolvar/InPlaneDistances.cpp
+++ b/src/multicolvar/InPlaneDistances.cpp
@@ -53,10 +53,10 @@ Keywords such as MORE_THAN and LESS_THAN can then be used to calculate the numbe
The following input can be used to calculate the number of atoms that have indices greater than 3 and less than 101 that
are within a cylinder with a radius of 0.3 nm that has its long axis aligned with the vector connecting atoms 1 and 2.
-\verbatim
+\plumedfile
d1: INPLANEDISTANCES VECTORSTART=1 VECTOREND=2 GROUP=3-100 LESS_THAN={RATIONAL D_0=0.2 R_0=0.1}
PRINT ARG=d1.lessthan FILE=colvar
-\endverbatim
+\endplumedfile
*/
diff --git a/src/multicolvar/LocalAverage.cpp b/src/multicolvar/LocalAverage.cpp
index fdc3e09c4f71cefa57e26558666d4de08ce494d4..c8bae1d56ed6e70460c2fdb8762a505621646603 100644
--- a/src/multicolvar/LocalAverage.cpp
+++ b/src/multicolvar/LocalAverage.cpp
@@ -59,21 +59,21 @@ and so on. You can also probe the value of these averaged variables in regions
This example input calculates the coordination numbers for all the atoms in the system. These coordination numbers are then averaged over
spherical regions. The number of averaged coordination numbers that are greater than 4 is then output to a file.
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=d1
LOCAL_AVERAGE ARG=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MORE_THAN={RATIONAL R_0=4} LABEL=la
PRINT ARG=la.* FILE=colvar
-\endverbatim
+\endplumedfile
This example input calculates the \f$q_4\f$ (see \ref Q4) vectors for each of the atoms in the system. These vectors are then averaged
component by component over a spherical region. The average value for this quantity is then outputeed to a file. This calculates the
quantities that were used in the paper by Lechner and Dellago \cite dellago-q6
-\verbatim
+\plumedfile
Q4 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=q4
LOCAL_AVERAGE ARG=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=la
PRINT ARG=la.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/MultiColvarDensity.cpp b/src/multicolvar/MultiColvarDensity.cpp
index 7ea3dc0096f3f8c2731cf885c94242efce8e3194..8e63b6e513a6043bc8e4edf8ee0a657a7142fbb5 100644
--- a/src/multicolvar/MultiColvarDensity.cpp
+++ b/src/multicolvar/MultiColvarDensity.cpp
@@ -58,11 +58,11 @@ The following example shows perhaps the simplest way in which this action can be
input computes the density of atoms at each point on the grid and ouptuts this quantity to a file. In
other words this input instructs plumed to calculate \f$\rho(\mathbf{r}) = \sum_i K(\mathbf{r} - \mathbf{r}_i )\f$
-\verbatim
+\plumedfile
dens: DENSITY SPECIES=1-100
grid: MULTICOLVARDENS DATA=dens ORIGIN=1 DIR=xyz NBINS=100,100,100 BANDWIDTH=0.05,0.05,0.05 STRIDE=1
DUMPGRID GRID=grid STRIDE=500 FILE=density
-\endverbatim
+\endplumedfile
In the above example density is added to the grid on every step. The PRINT_GRID instruction thus tells PLUMED to
output the average density at each point on the grid every 500 steps of simulation. Notice that the that grid output
@@ -72,11 +72,11 @@ of data separately you must use the CLEAR flag.
This second example computes an order parameter (in this case \ref FCCUBIC) and constructs a phase field model
for this order parameter using the equation above.
-\verbatim
+\plumedfile
fcc: FCCUBIC SPECIES=1-5184 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} ALPHA=27
dens: MULTICOLVARDENS DATA=fcc ORIGIN=1 DIR=xyz NBINS=14,14,28 BANDWIDTH=1.0,1.0,1.0 STRIDE=1 CLEAR=1
DUMPCUBE GRID=dens STRIDE=1 FILE=dens.cube
-\endverbatim
+\endplumedfile
In this example the phase field model is computed and output to a file on every step of the simulation. Furthermore,
because the CLEAR=1 keyword is set on the MULTICOLVARDENS line each Gaussian cube file output is a phase field
diff --git a/src/multicolvar/NumberOfLinks.cpp b/src/multicolvar/NumberOfLinks.cpp
index b8257c5e4b822510b0c2b6df77f6162297efa430..c8850755bdd7c7e54a672b66485deb188960bd84 100644
--- a/src/multicolvar/NumberOfLinks.cpp
+++ b/src/multicolvar/NumberOfLinks.cpp
@@ -43,22 +43,22 @@ similar orientations. The vectors on individual atoms could be Steinhardt param
The following calculates how many bonds there are in a system containing 64 atoms and outputs
this quantity to a file.
-\verbatim
+\plumedfile
DENSITY SPECIES=1-64 LABEL=d1
NLINKS ARG=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar
-\endverbatim
+\endplumedfile
The following calculates how many pairs of neighbouring atoms in a system containg 64 atoms have
similar dispositions for the atoms in their coordination sphere. This calculation uses the
dot product of the Q6 vectors on adjacent atoms to measure whether or not two atoms have the same
``orientation"
-\verbatim
+\plumedfile
Q6 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=q6
NLINKS ARG=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Torsions.cpp b/src/multicolvar/Torsions.cpp
index 59d02cbfd72ae82b03f05604ab1b851fa281856d..4e3fcfbb2d897de06b98b95ab2f6c854502a2d75 100644
--- a/src/multicolvar/Torsions.cpp
+++ b/src/multicolvar/Torsions.cpp
@@ -40,7 +40,7 @@ Calculate whether or not a set of torsional angles are within a particular range
The following provides an example of the input for the torsions command
-\verbatim
+\plumedfile
TORSIONS ...
ATOMS1=168,170,172,188
ATOMS2=170,172,188,190
@@ -48,13 +48,13 @@ ATOMS3=188,190,192,230
LABEL=ab
... TORSIONS
PRINT ARG=ab.* FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you
can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that you provide to this command to learn
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
TORSIONS ...
ATOMS1=@phi-3
@@ -63,7 +63,7 @@ ATOMS3=@phi-4
LABEL=ab
... TORSIONS
PRINT ARG=ab FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
diff --git a/src/multicolvar/VolumeAround.cpp b/src/multicolvar/VolumeAround.cpp
index bab79d8e0ab33d5893e78efe7fcf8202c19f8b09..d44f36d4b27857829b5a34877d8fa64a10c7e800 100644
--- a/src/multicolvar/VolumeAround.cpp
+++ b/src/multicolvar/VolumeAround.cpp
@@ -55,11 +55,11 @@ When AROUND is used with the \ref DENSITY action the number of atoms in the spec
The following commands tell plumed to calculate the average coordination number for the atoms
that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The final value will be labeled s.mean.
-\verbatim
+\plumedfile
COM ATOMS=1-100 LABEL=c1
COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 LABEL=c
AROUND DATA=c ORIGIN=c1 XLOWER=-2.0 XUPPER=2.0 SIGMA=0.1 MEAN LABEL=s
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeCavity.cpp b/src/multicolvar/VolumeCavity.cpp
index af14a2be05491eae1e3d06f0ef3bff612286ef16..70d8254f323433ae025019d363ee46254bbabac5 100644
--- a/src/multicolvar/VolumeCavity.cpp
+++ b/src/multicolvar/VolumeCavity.cpp
@@ -86,19 +86,19 @@ described above and the resulting projections determine the \f$u'\f$, \f$v'\f$ a
The following commands tell plumed to calculate the number of atoms in an ion chanel in a protein.
The extent of the chanel is calculated from the positions of atoms 1, 4, 5 and 11. The final value will be labeled cav.
-\verbatim
+\plumedfile
d1: DENSITY SPECIES=20-500
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav
-\endverbatim
+\endplumedfile
The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water
molecules in the protein channel described above. The average coordination number and the number of coordination
numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
-\verbatim
+\plumedfile
d1: COORDINATIONNUMBER SPECIES=20-500
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeInCylinder.cpp b/src/multicolvar/VolumeInCylinder.cpp
index eb6bc611e4cb7af7b3b3a3f55ab9fb5cd6a8f407..3e8acfb226ac8fcd2392c4b28d576b4eb23c2e68 100644
--- a/src/multicolvar/VolumeInCylinder.cpp
+++ b/src/multicolvar/VolumeInCylinder.cpp
@@ -59,11 +59,11 @@ When INCYLINDER is used with the \ref DENSITY action the number of atoms in the
The input below can be use to calculate the average coordination numbers for those atoms that are within a cylindrical tube
of radius 1.5 nm that is centered on the position of atom 101 and that has its long axis parallel to the z-axis.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
d2: INCYLINDER ATOM=101 DATA=d1 DIRECTION=Z RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 MEAN
PRINT ARG=d2.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeInSphere.cpp b/src/multicolvar/VolumeInSphere.cpp
index 632af88df5e7d799fe0fd9735c8a3a939ade215b..937e067dd82d68fcaedcb9321c353b2bf0e7f3ec 100644
--- a/src/multicolvar/VolumeInSphere.cpp
+++ b/src/multicolvar/VolumeInSphere.cpp
@@ -58,11 +58,11 @@ When INCYLINDER is used with the \ref DENSITY action the number of atoms in the
The input below can be use to calculate the average coordination numbers for those atoms that are within a sphere
of radius 1.5 nm that is centered on the position of atom 101.
-\verbatim
+\plumedfile
c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
d2: INSPHERE ATOM=101 DATA=d1 RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 MEAN
PRINT ARG=d2.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/VolumeTetrapore.cpp b/src/multicolvar/VolumeTetrapore.cpp
index 98fe915c33b7f55b5ee8b13ca983b2c12a97bcba..c7dcd66d04324e564adc15fd9a66a4faafb89787 100644
--- a/src/multicolvar/VolumeTetrapore.cpp
+++ b/src/multicolvar/VolumeTetrapore.cpp
@@ -94,19 +94,19 @@ This is in fact the only point of difference between these two actions.
The following commands tell plumed to calculate the number of atom inside a tetrahedral cavity. The extent of the tetrahedral
cavity is calculated from the positions of atoms 1, 4, 5, and 11, The final value will be labeled cav.
-\verbatim
+\plumedfile
d1: DENSITY SPECIES=20-500
TETRAHEDRALPORE DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav
-\endverbatim
+\endplumedfile
The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water
molecules in the tetrahedral cavity described above. The average coordination number and the number of coordination
numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
-\verbatim
+\plumedfile
d1: COORDINATIONNUMBER SPECIES=20-500
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/XAngle.cpp b/src/multicolvar/XAngle.cpp
index fbc2ab1d7104a9bb48620010dc2e633a5ce8d7e1..dd90c187f6f0fda16262a69a6df39e800316326c 100644
--- a/src/multicolvar/XAngle.cpp
+++ b/src/multicolvar/XAngle.cpp
@@ -41,10 +41,10 @@ Calculate the angles between the vector connecting two atoms and the x axis.
The following input tells plumed to calculate the angles between the x-axis and the vector connecting atom 3 to atom 5 and between the x-axis
and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
-\verbatim
+\plumedfile
XANLGES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -57,10 +57,10 @@ Calculate the angles between the vector connecting two atoms and the y axis.
The following input tells plumed to calculate the angles between the y-axis and the vector connecting atom 3 to atom 5 and between the y-axis
and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
-\verbatim
+\plumedfile
YANLGES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -73,10 +73,10 @@ Calculate the angles between the vector connecting two atoms and the z axis.
The following input tells plumed to calculate the angles between the z-axis and the vector connecting atom 3 to atom 5 and between the z-axis
and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
-\verbatim
+\plumedfile
ZANLGES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/XDistances.cpp b/src/multicolvar/XDistances.cpp
index 009b04de595c7f0a84f1566e07664769a34e1126..fe29a8b650baa8c14f47157ce4fa40f3e88191af 100644
--- a/src/multicolvar/XDistances.cpp
+++ b/src/multicolvar/XDistances.cpp
@@ -42,38 +42,38 @@ values such as the minimum, the number less than a certain quantity and so on.
The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
the x-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and
the x-component of the vector connecting atom 1 to atom 2. The number of values that are
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
XDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate the x-components of all the distinct vectors that can be created
between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
The average of these quantities is then calculated.
-\verbatim
+\plumedfile
XDISTANCES GROUP=1-3 AVERAGE LABEL=d1
PRINT ARG=d1.average
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
XDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
*/
//+ENDPLUMEDOC
@@ -89,38 +89,38 @@ values such as the minimum, the number less than a certain quantity and so on.
The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
the y-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and
the y-component of the vector connecting atom 1 to atom 2. The number of values that are
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
YDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate the y-components of all the distinct vectors that can be created
between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
The average of these quantities is then calculated.
-\verbatim
+\plumedfile
YDISTANCES GROUP=1-3 AVERAGE LABEL=d1
PRINT ARG=d1.average
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
YDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
*/
@@ -137,38 +137,38 @@ values such as the minimum, the number less than a certain quantity and so on.
The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
the z-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and
the z-component of the vector connecting atom 1 to atom 2. The number of values that are
less than 0.1nm is then printed to a file.
-\verbatim
+\plumedfile
ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.lt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction).
The following input tells plumed to calculate the z-components of all the distinct vectors that can be created
between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).
The average of these quantities is then calculated.
-\verbatim
+\plumedfile
ZDISTANCES GROUP=1-3 AVERAGE LABEL=d1
PRINT ARG=d1.average
-\endverbatim
+\endplumedfile
(See also \ref PRINT)
The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.
In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3. The number of values
more than 0.1 is then printed to a file.
-\verbatim
+\plumedfile
ZDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
PRINT ARG=d1.gt0.1
-\endverbatim
+\endplumedfile
(See also \ref PRINT \ref switchingfunction)
*/
diff --git a/src/multicolvar/XYDistances.cpp b/src/multicolvar/XYDistances.cpp
index 767c64a86aafc268d23c4f0bce0c6f5bf80c1b4d..c0c8d4aa5272b49f7f1a05ab674fb1e3faa38f44 100644
--- a/src/multicolvar/XYDistances.cpp
+++ b/src/multicolvar/XYDistances.cpp
@@ -43,10 +43,10 @@ The following input tells plumed to calculate the projection of the length of th
to atom 5 projected in the xy-plane and the projection of the length of the vector
the vector connecting atom 1 to atom 2 in the xy-plane. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
@@ -64,10 +64,10 @@ The following input tells plumed to calculate the projection of the length of th
to atom 5 projected in the xz-plane and the projection of the length of the vector
the vector connecting atom 1 to atom 2 in the xz-plane. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
@@ -85,10 +85,10 @@ The following input tells plumed to calculate the projection of the length of th
to atom 5 in the yz-plane and the projection of the length of the vector
the vector connecting atom 1 to atom 2 in the yz-plane. The minimum of these two quantities is then
printed
-\verbatim
+\plumedfile
YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
diff --git a/src/multicolvar/XYTorsion.cpp b/src/multicolvar/XYTorsion.cpp
index fd512799a44f1e8121994fbb61b0ff8e3b708638..4e0804a508811722ae292890ea8c1b0ed1db84d4 100644
--- a/src/multicolvar/XYTorsion.cpp
+++ b/src/multicolvar/XYTorsion.cpp
@@ -41,10 +41,10 @@ Calculate the torsional angle around the x axis from the positive y direction.
The following input tells plumed to calculate the angle around the x direction between the positive y-axis and the vector connecting atom 3 to atom 5 and
the angle around the x direction between the positive y axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -57,10 +57,10 @@ Calculate the torsional angle around the x axis from the positive z direction.
The following input tells plumed to calculate the angle around the x direction between the positive z-axis and the vector connecting atom 3 to atom 5 and
the angle around the x direction between the positive z direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -73,10 +73,10 @@ Calculate the torsional angle around the y axis from the positive x direction.
The following input tells plumed to calculate the angle around the y direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
the angle around the y direction between the positive x axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -89,10 +89,10 @@ Calculate the torsional angle around the y axis from the positive z direction.
The following input tells plumed to calculate the angle around the y direction between the positive z-direction and the vector connecting atom 3 to atom 5 and
the angle around the y direction between the positive z direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -105,10 +105,10 @@ Calculate the torsional angle around the z axis from the positive x direction.
The following input tells plumed to calculate the angle around the z direction between the positive x-direction and the vector connecting atom 3 to atom 5 and
the angle around the z direction between the positive x-direction and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
@@ -121,10 +121,10 @@ Calculate the torsional angle around the z axis from the positive y direction.
The following input tells plumed to calculate the angle around the z direction between the positive y-axis and the vector connecting atom 3 to atom 5 and
the angle around the z direction between the positive y axis and the vector connecting atom 1 to atom 2. The minimum of these two quantities is then output
-\verbatim
+\plumedfile
ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
PRINT ARG=d1.min
-\endverbatim
+\endplumedfile
(See also \ref PRINT).
*/
//+ENDPLUMEDOC
diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp
index 6c9b49083ea11d2bc3f49863ab4984125333b8a6..ecf10eacb32de321aa4b63b509c050279713080b 100644
--- a/src/secondarystructure/AlphaRMSD.cpp
+++ b/src/secondarystructure/AlphaRMSD.cpp
@@ -68,11 +68,10 @@ anthing other than TYPE=DRMSD. For more details as to how to do this see \ref W
The following input calculates the number of six residue segments of
protein that are in an alpha helical configuration.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index 6e60d54454e0d60860f6322d9e4e30e900938a7f..637e4c0b38522f58aec85f9860ac058964c0c6e9 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -70,11 +70,10 @@ anthing other than TYPE=DRMSD. For more details as to how to do this see \ref W
The following input calculates the number of six residue segments of
protein that are in an antiparallel beta sheet configuration.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
ANTIBETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index fe87408643184d808adea19581f33671f7b78435..1a67ec8afcf6de744c7b99882055c7731615ddea 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -70,11 +70,10 @@ anthing other than TYPE=DRMSD. For more details as to how to do this see \ref W
The following input calculates the number of six residue segments of
protein that are in an parallel beta sheet configuration.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=helix.pdb
PARABETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref MOLINFO)
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/setup/Load.cpp b/src/setup/Load.cpp
index 93f9d39b8831e7e18e926b3b61b0e01e66ce6b62..4002ed0f0ff6671d04b5f9d9aa7ef1068e13e027 100644
--- a/src/setup/Load.cpp
+++ b/src/setup/Load.cpp
@@ -43,9 +43,9 @@ If you have a shared object named extensions.so and want to
use the functionalities implemented in it within PLUMED you can
load it with the following syntax
-\verbatim
+\plumedfile
LOAD FILE=extensions.so
-\endverbatim
+\endplumedfile
As a more practical example, imagine that you want to make a
small change to one collective variable that is already implemented
@@ -61,7 +61,7 @@ with different names. Then you can compile it into a shared object using
This will generate a file `Distance2.so` (or `Distance2.dylib` on a mac)
that can be loaded.
Now you can use your new implementation with the following input
-\verbatim
+\plumedfile
# load the new library
LOAD FILE=Distance2.so
# compute standard distance
@@ -70,11 +70,11 @@ d: DISTANCE ATOMS=1,10
d2: DISTANCE2 ATOMS=1,10
# print them on a file
PRINT ARG=d,d2 FILE=compare-them
-\endverbatim
+\endplumedfile
You can even skip the initial step and directly feed PLUMED
with the `Distance2.cpp` file: it will be compiled on the fly.
-\verbatim
+\plumedfile
# load the new definition
# this is a cpp file so it will be compiled
LOAD FILE=Distance2.cpp
@@ -84,7 +84,7 @@ d: DISTANCE ATOMS=1,10
d2: DISTANCE2 ATOMS=1,10
# print them on a file
PRINT ARG=d,d2 FILE=compare-them
-\endverbatim
+\endplumedfile
This will allow to make quick tests while developing your own
variables. Of course, after your implementation is ready you might
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
index 03a0012f97a8eaac8c5561aa7fa55f303f718282..32210012db83e1581b5ff1994a663b2f7c89867b 100644
--- a/src/setup/MolInfo.cpp
+++ b/src/setup/MolInfo.cpp
@@ -37,12 +37,14 @@ then use this information in later commands to specify atom lists in terms resid
using this command you can find the backbone atoms in your structure automatically.
\warning
-Please be aware that the pdb parser in plumed is far from perfect. You should thus check the log file
+Please be aware that the PDB parser in plumed is far from perfect. You should thus check the log file
and examine what plumed is actually doing whenenver you use the MOLINFO action.
Also make sure that the atoms are listed in the pdb with the correct order.
If you are using gromacs, the safest way is to use reference pdb file
generated with `gmx editconf -f topol.tpr -o reference.pdb`.
+More information of the PDB parser implemented in PLUMED can be found \ref pdbreader "at this page".
+
Using MOLINFO with a protein's or nucleic acid's pdb extends the possibility of atoms selection using the @ special
symbol.
@@ -111,23 +113,21 @@ interpret terminal residue 1.
In the following example the MOLINFO command is used to provide the information on which atoms
are in the backbone of a protein to the ALPHARMSD CV.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=reference.pdb
ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
-\endverbatim
-(see also \ref ALPHARMSD)
+\endplumedfile
The following example prints the distance corresponding to the hydrogen bonds
in a GC Watson-Crick pair.
-\verbatim
+\plumedfile
MOLINFO STRUCTURE=reference.pdb
hb1: DISTANCE ATOMS=@N2-1,@O2-14
hb2: DISTANCE ATOMS=@N1-1,@N3-14
hb3: DISTANCE ATOMS=@O6-1,@N4-14
PRINT ARG=hb1,hb2,hb3
-\endverbatim
-(see also \ref DISTANCE).
+\endplumedfile
*/
diff --git a/src/setup/Restart.cpp b/src/setup/Restart.cpp
index ffa4f46b1b4487f628f4dea4d9965778378369c1..c33bbe1a4ff7a975b468ce15cc4cf7a0da5818af 100644
--- a/src/setup/Restart.cpp
+++ b/src/setup/Restart.cpp
@@ -51,31 +51,38 @@ and \ref PBMETAD and on some analysis action.
\par Examples
Using the following input:
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=out
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
a new 'out' file will be created. If an old one is on the way, it will be automatically backed up.
On the other hand, using the following input:
-\verbatim
+\plumedfile
RESTART
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=out
-\endverbatim
+\endplumedfile
the file 'out' will be appended.
-(See also \ref DISTANCE and \ref PRINT).
In the following case, file out1 will be backed up and file out2 will be concatenated
-\verbatim
+\plumedfile
RESTART
d1: DISTANCE ATOMS=1,2
d2: DISTANCE ATOMS=1,2
PRINT ARG=d1 FILE=out1 RESTART=NO
PRINT ARG=d2 FILE=out2
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
+
+In the following case, file out will backed up even if the MD code thinks that we
+are restarting. Notice that not all the MD code send to PLUMED information about restarts.
+If you are not sure, always put `RESTART` when you are restarting and nothing when you aren't
+\plumedfile
+RESTART NO
+d1: DISTANCE ATOMS=1,2
+PRINT ARG=d1 FILE=out1
+\endplumedfile
+
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index 1b4225d24482ef09d48d08da5561b24f48b8e1cb..edd45fe4f9e24436f8784cc71c6c5c5d0dcc63bf 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -44,16 +44,36 @@ the units. For example, trajectories written in .gro format (with \ref DUMPATOMS
are going to be always in nm.
\par Examples
-\verbatim
-# this is using nm - kj/mol - fs
-UNITS LENGTH=nm TIME=fs
-\endverbatim
-If a number, x, is found, the new unit is equal to x (default units)
-\verbatim
+
+
+\plumedfile
# this is using nm - kj/mol - fs
-UNITS LENGTH=nm TIME=0.001
-\endverbatim
+UNITS LENGTH=A TIME=fs
+
+# compute distance between atoms 1 and 4
+d: DISTANCE ATOMS=1,4
+
+# print time and distance on a COLVAR file
+PRINT ARG=d FILE=COLVAR
+
+# dump atoms 1 to 100 on a 'out.gro' file
+DUMPATOMS FILE=out.gro STRIDE=10 ATOMS=1-100
+
+# dump atoms 1 to 100 on a 'out.xyz' file
+DUMPATOMS FILE=out.xyz STRIDE=10 ATOMS=1-100
+\endplumedfile
+
+In the `COLVAR` file, time and distance will appear in fs and A respectively, *irrespectively* of which units
+you are using the the host MD code. The coordinates in the `out.gro` file will be expressed in nm,
+since `gro` files are by convention written in nm. The coordinates in the `out.xyz` file
+will be written in Angstrom *since we used the UNITS command setting Angstrom units*.
+Indeed, within PLUMED xyz files are using internal PLUMED units and not necessarily Angstrom!
+If a number, x, is found instead of a string, the new unit is equal to x times the default units.
+Using the following command as first line of the previous example would have lead to an identical result:
+\plumedfile
+UNITS LENGTH=0.1 TIME=0.001
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/tools/PDB.cpp b/src/tools/PDB.cpp
index 128e4620e94e3cee32081c0b43bf7bf2dd4dc7a7..cb90135ab5da8090112a8f00367df74264a0afc7 100644
--- a/src/tools/PDB.cpp
+++ b/src/tools/PDB.cpp
@@ -27,6 +27,76 @@
using namespace std;
+//+PLUMEDOC INTERNAL pdbreader
+/*
+
+PLUMED use PDB formats in several places, including
+- To read molecular structure (\ref MOLINFO).
+- To read reference conformations (\ref RMSD, but also many other methods in \ref dists, \ref FIT_TO_TEMPLATE, etc).
+
+The implemented PDB reader expects a file formatted correctly according to the
+[PDB standard](http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html).
+In particular, the following columns are read from ATOM records
+\verbatim
+columns | content
+1-6 | record name (ATOM or HETATM)
+7-11 | serial number of the atom (starting from 1)
+13-16 | atom name
+18-20 | residue name
+22 | chain id
+23-26 | residue number
+31-38 | x coordinate
+39-46 | y coordinate
+47-54 | z coordinate
+55-60 | occupancy
+61-66 | beta factor
+\endverbatim
+PLUMED parser is slightly more permissive than the official PDB format
+in the fact that the format of real numbers is not fixed. In other words,
+any parsable real number is ok and the dot can be placed anywhere. However,
+__columns are interpret strictly__. A sample PDB should look like the following
+\verbatim
+ATOM 2 CH3 ACE 1 12.932 -14.718 -6.016 1.00 1.00
+ATOM 5 C ACE 1 21.312 -9.928 -5.946 1.00 1.00
+ATOM 9 CA ALA 2 19.462 -11.088 -8.986 1.00 1.00
+\endverbatim
+
+Notice that serial numbers need not to be consecutive. In the three-line example above,
+only the coordinates of three atoms are provided. This is perfectly legal and indicates PLUMED
+that information about these atoms only is available. This could be both for structural
+information in \ref MOLINFO, where the other atoms would have no name assigned, and for
+reference structures used in \ref RMSD, where only the provided atoms would be used to compute RMSD.
+
+\par Occupancy and beta factors
+
+PLUMED reads also occupancy and beta factors that however are given a very special meaning.
+In cases where the PDB structure is used as a reference for an alignment (that's the case
+for instance in \ref RMSD and in \ref FIT_TO_TEMPLATE), the occupancy column is used
+to provide the weight of each atom in the alignment. In cases where, perhaps after alignment,
+the displacement between running coordinates and the provided PDB is computed, the beta factors
+are used as weight for the displacement.
+Since setting the weights to zero is the same as __not__ including an atom in the alignement or
+displacement calculation, the two following reference files would be equivalent when used in an \ref RMSD
+calculation. First file:
+\verbatim
+ATOM 2 CH3 ACE 1 12.932 -14.718 -6.016 1.00 1.00
+ATOM 5 C ACE 1 21.312 -9.928 -5.946 1.00 1.00
+ATOM 9 CA ALA 2 19.462 -11.088 -8.986 0.00 0.00
+\endverbatim
+Second file:
+\verbatim
+ATOM 2 CH3 ACE 1 12.932 -14.718 -6.016 1.00 1.00
+ATOM 5 C ACE 1 21.312 -9.928 -5.946 1.00 1.00
+\endverbatim
+However notice that many extra atoms with zero weight might slow down the calculation, so
+removing lines is better than setting their weights to zero.
+In addition, weights for alignment need not to be equivalent to weights for displacement.
+
+
+*/
+//+ENDPLUMEDOC
+
+
namespace PLMD {
/// Tiny namespace for hybrid36 format.
diff --git a/src/vatom/COM.cpp b/src/vatom/COM.cpp
index f9334eb6b676914d389b279e0adf5d270a6260ea..d0cfd0b1feffc1f163e57309aca191192d738157 100644
--- a/src/vatom/COM.cpp
+++ b/src/vatom/COM.cpp
@@ -54,13 +54,12 @@ periodic image.
The following input instructs plumed to print the distance between the
center of mass for atoms 1,2,3,4,5,6,7 and that for atoms 15,20:
-\verbatim
-COM ATOMS=1-7 LABEL=c1
-COM ATOMS=15,20 LABEL=c2
-DISTANCE ATOMS=c1,c2 LABEL=d1
+\plumedfile
+c1: COM ATOMS=1-7
+c2: COM ATOMS=15,20
+d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/vatom/Center.cpp b/src/vatom/Center.cpp
index 7e4cdd440239f6dbe9ef99ced9da6d836017dacc..64eea7d7419381476acfa879d1640cd38fdc8d79 100644
--- a/src/vatom/Center.cpp
+++ b/src/vatom/Center.cpp
@@ -54,7 +54,7 @@ periodic image.
\par Examples
-\verbatim
+\plumedfile
# a point which is on the line connecting atoms 1 and 10, so that its distance
# from 10 is twice its distance from 1:
c1: CENTER ATOMS=1,1,10
@@ -67,8 +67,7 @@ c2: CENTER ATOMS=2,3,4,5 MASS
d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1
-\endverbatim
-(See also \ref DISTANCE, \ref COM and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/vatom/FixedAtom.cpp b/src/vatom/FixedAtom.cpp
index ccf7eb52ca84063a68e269607643d8d4bc81c1b4..3baf40379a1c7c7f271c33e5563d16d7878ff8c6 100644
--- a/src/vatom/FixedAtom.cpp
+++ b/src/vatom/FixedAtom.cpp
@@ -51,24 +51,22 @@ then it is safe to add further fixed atoms without breaking translational invari
The following input instructs plumed to compute the angle between
distance of atoms 15 and 20 and the z axis and keeping it close to zero.
-\verbatim
+\plumedfile
a: FIXEDATOM AT=0,0,0
b: FIXEDATOM AT=0,0,1
an: ANGLE ATOMS=a,b,15,20
RESTRAINT ARG=an AT=0.0 KAPPA=100.0
-\endverbatim
-(See also \ref ANGLE and \ref RESTRAINT).
+\endplumedfile
The following input instructs plumed to align a protein on a template
and then compute the distance of one of its atom from the point
(10,20,30).
-\verbatim
+\plumedfile
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE
a: FIXEDATOM AT=10,20,30
d: DISTANCE ARG=a,20
PRINT ARG=d FILE=colvar
-\endverbatim
-(See also \ref FIT_TO_TEMPLATE and \ref DISTANCE).
+\endplumedfile
*/
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index fcd78937756a436870700484a157a3b943bf5f74..7c57cee4ffad29f228ab766fd241a685065e0134 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -39,13 +39,12 @@ an atom list through the the label for the GHOST action that creates it.
\par Examples
The following input instructs plumed to print the distance between the
ghost atom and the center of mass for atoms 15,20:
-\verbatim
-GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0 LABEL=c1
-COM ATOMS=15,20 LABEL=c2
-DISTANCE ATOMS=c1,c2 LABEL=d1
+\plumedfile
+c1: GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0
+c2: COM ATOMS=15,20
+d1: DISTANCE ATOMS=c1,c2
PRINT ARG=d1
-\endverbatim
-(See also \ref DISTANCE and \ref PRINT).
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/user-doc/Analysis.txt b/user-doc/Analysis.txt
index a5a0e55729a80ac63bba00f7ee2844e9b33694ed..ef3a005893acfb9f66e3f5bcfc294c8c73f96456 100644
--- a/user-doc/Analysis.txt
+++ b/user-doc/Analysis.txt
@@ -45,11 +45,11 @@ As an example the following set of commands instructs PLUMED to calculate the di
atoms 1 and 2 for every 5th frame in the trajectory and to accumulate a histogram from this data
which will be output every 100 steps (i.e. when 20 distances have been added to the histogram).
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
h: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1 STRIDE=5
DUMPGRID GRID=h FILE=histo STRIDE=100
-\endverbatim
+\endplumedfile
It is important to note when using commands such as the above the first frame in the trajectory is assumed
to be the initial configuration that was input to the MD code. It is thus ignored. Furthermore, if you are
@@ -57,11 +57,11 @@ running with driver and you would like to analyse the whole trajectory (without
and then print the result you simply call \ref DUMPGRID (or any of the commands above) without a STRIDE
keyword as shown in the example below.
-\verbatim
+\plumedfile
x: DISTANCE ATOMS=1,2
h: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1 STRIDE=5
DUMPGRID GRID=h FILE=histo
-\endverbatim
+\endplumedfile
Please note that even with this calculation the first frame in the trajectory is ignored when computing the
histogram.
diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
index 7c6557796d1e5f042bd893987976443b627b175e..ab0d3a2f3c3c3483f18460cb72a8765d36e7b5d9 100644
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
@@ -58,6 +58,8 @@ with the ammount the collective variables change. A full list of the ways dista
These options for calculating distances are re-used in a number of places in the code. For instance they are used in some of the
analysis algorithms that are implemented in PLUMED and in \ref PATH collective variables.
+Notice that most of these actions read the reference configuration from a PDB file. Be sure
+you understand how to format properly a PDB file to use used in PLUMED (see \ref pdbreader).
\page mcolv MultiColvar
@@ -92,9 +94,9 @@ Oftentimes the simplest way to specify the atoms involved is to use multiple ins
i.e. ATOMS1, ATOMS2, ATOMS3,... Separate instances of the quantity specified by NAME are then calculated for
each of the sets of atoms. For example if the command issued contains the following:
-\verbatim
+\plumedfile
DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6
-\endverbatim
+\endplumedfile
The distances between atoms 1 and 2, atoms 3 and 4, and atoms 5 and 6 are calculated. Obviously, generating
this sort of input is rather tedious so short cuts are also available many of the collective variables.
@@ -163,11 +165,11 @@ prevent the cluster subliming. Alternatively, you may wish to insist that a par
coordination number greater than 2. You can add these sorts of restraints by employing the following biases, which all act
on the set of collective variable values calculated by a multicolvar. So for example the following set of commands:
-\verbatim
+\plumedfile
COM ATOMS=1-20 LABEL=c1
DISTANCES GROUPA=c1 GROUPB=1-20 LABEL=d1
UWALLS DATA=d1 AT=2.5 KAPPA=0.2 LABEL=sr
-\endverbatim
+\endplumedfile
creates the aforementioned set of restraints on the distances between the 20 atoms in a cluster and the center of mass of the cluster.
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index fdcd5c47715b2c7abb02b77fc52a7797d9d77f5a..7a884face6c60aff15d88b8b1b61eb0a5e1a50cc 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -228,11 +228,17 @@ TAB_SIZE = 8
# "Side Effects:". You can put \n's in the value part of an alias to insert
# newlines.
-ALIASES = "hidden=\htmlonly <details> <summary> <b> To learn more </b> </summary> <div class=\"hidden\"> \endhtmlonly" \
+ALIASES = \
+ "hidden=\htmlonly <details> <summary> <b> To learn more </b> </summary> <div class=\"hidden\"> \endhtmlonly" \
"hidden{1}=\htmlonly <details> <summary> <b> To learn more: \1 </b> </summary> <div class=\"hidden\"> \endhtmlonly" \
"endhidden=\htmlonly </div> </details> \endhtmlonly" \
"issue{1}=<a href=\"http://github.com/plumed/plumed2/issues/\1\">#\1</a>" \
- "branch{1}=<a href=\"http://github.com/plumed/plumed2/commits/\1\">\1</a>"
+ "branch{1}=<a href=\"http://github.com/plumed/plumed2/commits/\1\">\1</a>" \
+ "highlight{1}=\htmlonly<span style=\"background-color:yellow\">\endhtmlonly\1\htmlonly</span>\endhtmlonly" \
+ "tarball{1}=<a href=\"tutorial-resources/\1.tar.gz\" style=\"font-weight:bold\" style=\"color:green\" download=\"\1.tar.gz\"> TARBALL </a>" \
+ "plumedfile=\verbatim BEGIN_PLUMED_FILE" \
+ "endplumedfile=\endverbatim"
+
# This tag can be used to specify a number of word-keyword mappings (TCL only).
# A mapping has the form "name=value". For example adding "class=itcl::class"
diff --git a/user-doc/Files.txt b/user-doc/Files.txt
index f360af5d28e4a86540994c23ef7ce69bd9e6d5ca..2ed8f21ee892fb39d4d1419bff7ddbdf3e3c0ee2 100644
--- a/user-doc/Files.txt
+++ b/user-doc/Files.txt
@@ -34,11 +34,10 @@ since your disk might fill up quickly with this setting.
When running with multiple replicas (e.g., with GROMACS, -multi option) PLUMED adds the replica index as a suffix to
all the files. The following command
will thus print files named COLVAR.0, COLVAR.1, etc for the different replicas.
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=COLVAR
-\endverbatim
-(see also \ref DISTANCE and \ref PRINT).
+\endplumedfile
When reading a file, PLUMED will try to add the suffix. If the file is not found, it will fall back to
the name without suffix. The most important case is the reading of the plumed input file.
@@ -51,12 +50,11 @@ extension. Before PLUMED 2.2, the only recognized suffix was ".gz". Since 2.2, a
less or equal to five letters is recognized.
This means that using in a multireplica context an input such as
-\verbatim
+\plumedfile
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=COLVAR.gz
METAD ARG=d FILE=test.HILLS SIGMA=0.1 HEIGHT=0.1
-\endverbatim
-(see \ref DISTANCE, \ref PRINT, and \ref METAD)
+\endplumedfile
PLUMED will write files named COLVAR.0.gz, COLVAR.1.gz, test.0.HILLS, test.1.HILLS, etc
etc. This is useful since the preserved extension makes it easy
to process the files later.
diff --git a/user-doc/Functions.txt b/user-doc/Functions.txt
index 8bf37c42db0e66f5e2727bb98b419edeb4f88217..53de40f365fef8acff528a4a3d0596dd259e7db4 100644
--- a/user-doc/Functions.txt
+++ b/user-doc/Functions.txt
@@ -23,7 +23,7 @@ is the smallest value and `B` is the largest value. In case the answer is that t
values at the discontinuity are not always the same, then you cannot construct a variable that
can be biased with PLUMED. Consider the following examples:
-\verbatim
+\plumedfile
t: TORSION ATOMS=1,2,3,4
# When atoms are moved, t could jump suddenly from -pi to +pi
@@ -39,7 +39,7 @@ d: DISTANCE ATOMS=1,10 COMPONENTS
# make a new variable equal to d.z but with the correct periodicity
dz: COMBINE ARG=d.z PERIODIC=-10,10
# here we assumed the system is in a orthorhombic box with z side = 20
-\endverbatim
+\endplumedfile
@FUNCTION@
diff --git a/user-doc/Group.txt b/user-doc/Group.txt
index 6365d9f7dd91b987cb4588a4fb6ab2a1b80610df..6edc0225b513c21370ca85c0f3712589ab624ce1 100644
--- a/user-doc/Group.txt
+++ b/user-doc/Group.txt
@@ -56,12 +56,12 @@ See http://en.wikipedia.org/wiki/Ramachandran_plot
The following example shows how to use \ref MOLINFO with \ref TORSION to calculate the torsion angles phi and psi for the first and fourth residue
of the protein:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
PRINT ARG=t1,t2 FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
\subsection pbc Broken Molecules and PBC
@@ -76,11 +76,11 @@ using the ALIGN_ATOMS keyword. In PLUMED 2 the same effect can be achieved usin
The following input computes the end-to-end distance for a polymer of 100 atoms and keeps it at a value around 5.
-\verbatim
+\plumedfile
WHOLEMOLECULES ENTITY0=1-100
e2e: DISTANCE ATOMS=1,100 NOPBC
RESTRAINT ARG=e2e KAPPA=1 AT=5
-\endverbatim
+\endplumedfile
Notice that NOPBC is used to be sure in \ref DISTANCE that if the end-to-end distance is larger than half the simulation box the distance
is compute properly. Also notice that, since many MD codes break molecules across cell boundary, it might be necessary to use the
@@ -90,12 +90,12 @@ Notice that most expressions are invariant with respect to a change in the order
but some of them depend on that order. E.g., with \ref WHOLEMOLECULES it could be useful to
specify atom lists in a reversed order.
-\verbatim
+\plumedfile
# to see the effect, one could dump the atoms as they were before molecule reconstruction:
# DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20
WHOLEMOLECULES STRIDE=1 ENTITY0=1-20
DUMPATOMS FILE=dump.xyz ATOMS=1-20
-\endverbatim
+\endplumedfile
Notice that there are other ways to manipulate the coordinates stored within PLUMED:
- Using the \subpage FIT_TO_TEMPLATE they can be aligned to a template structure.
@@ -116,10 +116,10 @@ To specify to a colvar that you want to use the position of a virtual atom to ca
in your system you simply use the label for your virtual atom in place of the usual numerical index. Virtual
atoms and normal atoms can be mixed together in the input to colvars as shown below:
-\verbatim
+\plumedfile
COM ATOMS=1,10 LABEL=com1
DISTANCE ATOMS=11,com1
-\endverbatim
+\endplumedfile
If you don't want to calculate CVs from the virtual atom. That is to say you just want to monitor the position of a virtual atom
(or any set of atoms) over the course of your trajectory you can do this using \ref DUMPATOMS.
diff --git a/user-doc/Misc.txt b/user-doc/Misc.txt
index 284a2a6e9bdfc65ce0b7e12f698bafd089cea19d..4fceb133df2803ed71979ab1277ea6c00c770dc7 100644
--- a/user-doc/Misc.txt
+++ b/user-doc/Misc.txt
@@ -19,12 +19,12 @@ particular simulation you might find it useful to put comments in your input fil
comments can be added using a # sign. On any given line everything after the # sign is ignored so
erm... yes add lines of comments or trailing comments to your hearts content as shown below (using Shakespeare is optional):
-\verbatim
+\plumedfile
# 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.
-\endverbatim
+\endplumedfile
(see \ref DISTANCE and \ref UPPER_WALLS)
An alternative to including comments in this way is to use line starting ENDPLUMED. Everything in the PLUMED input after this
@@ -37,14 +37,14 @@ We at PLUMED are aware of this fact and thus have provided a way of doing line c
easier - aren't we kind? Well no not really, we have to use this code too. Anyway, you can do continuations by using the "..." syntax
as this makes this:
-\verbatim
+\plumedfile
DISTANCES ATOMS1=1,300 ATOMS2=1,400 ATOMS3=1,500 LABEL=dist
-\endverbatim
+\endplumedfile
(see \ref DISTANCES)
equivalent to this:
-\verbatim
+\plumedfile
DISTANCES ...
LABEL=dist
# we can also insert comments here
@@ -54,11 +54,11 @@ DISTANCES ...
#empty lines are also allowed
... DISTANCES
-\endverbatim
+\endplumedfile
Notice that the closing `...` is followed by the word `DISTANCES`. This is optional, but might be
useful to find more easily which is the matching start of the statement. The following is equally correct
-\verbatim
+\plumedfile
DISTANCES ...
LABEL=dist
# we can also insert comments here
@@ -68,12 +68,12 @@ DISTANCES ...
#empty lines are also allowed
...
-\endverbatim
+\endplumedfile
Notice that PLUMED makes a check that the word following the closing `...` is actually identical to
the first word in the line with the first `...`. If not, it will throw an error.
Also notice that you might put more than one word in the first line. E.g.
-\verbatim
+\plumedfile
DISTANCES LABEL=dist ...
# we can also insert comments here
ATOMS1=1,300
@@ -81,9 +81,9 @@ DISTANCES LABEL=dist ...
ATOMS2=1,400 ATOMS3=1,500
#empty lines are also allowed
...
-\endverbatim
+\endplumedfile
or, equivalently,
-\verbatim
+\plumedfile
dist: DISTANCES ...
# we can also insert comments here
ATOMS1=1,300
@@ -91,7 +91,7 @@ dist: DISTANCES ...
ATOMS2=1,400 ATOMS3=1,500
#empty lines are also allowed
...
-\endverbatim
+\endplumedfile
\page VimSyntax Using VIM syntax file
@@ -171,11 +171,11 @@ Add to your `.vimrc` file the following commands
:set modelines=5
\endverbatim
Then, at the beginning of your PLUMED input file, put the following comment:
-\verbatim
+\plumedfile
# vim:ft=plumed
d: DISTANCE ATOMS=1,2
RESTRAINT ARG=d AT=0.0 KAPPA=1.0
-\endverbatim
+\endplumedfile
Now, every time you open this file, you will see it highlighted.
\par Syntax highlighting
@@ -220,27 +220,27 @@ Folded lines can be expanded with `zo` and folded with `zc`. Look at VIM documen
learn more.
In case you want to use this feature, we suggest you to put both label
and action type on the first line of multi-line statements. E.g.
-\verbatim
+\plumedfile
m: METAD ...
ARG=d
HEIGHT=1.0
SIGMA=0.5
PACE=100
...
-\endverbatim
+\endplumedfile
will be folded to
\verbatim
+-- 6 lines: m: METAD ...------------------------------------------------------
\endverbatim
and
-\verbatim
+\plumedfile
METAD LABEL=m ...
ARG=d
HEIGHT=1.0
SIGMA=0.5
PACE=100
...
-\endverbatim
+\endplumedfile
will be folded to
\verbatim
+-- 6 lines: METAD LABEL=m ...-------------------------------------------------
@@ -293,9 +293,9 @@ Try to do the following. Enable plumed syntax:
:set ft=plumed
\endverbatim
Then add the following line
-\verbatim
+\plumedfile
DISTANCE
-\endverbatim
+\endplumedfile
Now, in normal mode, go with the cursor on the `DISTANCE` line and type
\verbatim
:PHelp
@@ -365,38 +365,37 @@ vimrc file.
If, for some reason, you want to spread your PLUMED input over a number of files you can use \subpage INCLUDE as shown below:
-\verbatim
+\plumedfile
INCLUDE FILE=filename
-\endverbatim
+\endplumedfile
So, for example, a single "plumed.dat" file:
-\verbatim
+\plumedfile
DISTANCE ATOMS=0,1 LABEL=dist
RESTRAINT ARG=dist
-\endverbatim
-(see \ref DISTANCE and \ref RESTRAINT)
+\endplumedfile
could be split up into two files as shown below:
-\verbatim
+\plumedfile
DISTANCE ATOMS=0,1 LABEL=dist
INCLUDE FILE=toBeIncluded.dat
-\endverbatim
+\endplumedfile
plus a "toBeIncluded.dat" file
-\verbatim
+\plumedfile
RESTRAINT ARG=dist
-\endverbatim
+\endplumedfile
However, when you do this it is important to recognise that \ref INCLUDE is a real directive that is only resolved
after all the \ref comments have been stripped and the \ref ContinuationLines have been unrolled. This means it
is not possible to do things like:
-\verbatim
+\plumedfile
# this is wrong:
DISTANCE INCLUDE FILE=options.dat
RESTRAINT ARG=dist
-\endverbatim
+\endplumedfile
\page load Loading shared libraries
@@ -405,9 +404,9 @@ PLUMED libraries. Alternatively, if you want to keep your code independent from
so you can release it independely - we won't be offended), then you can create your own dynamic library. To use this
in conjuction with PLUMED you can then load it at runtime by using the \subpage LOAD keyword as shown below:
-\verbatim
+\plumedfile
LOAD FILE=library.so
-\endverbatim
+\endplumedfile
N.B. If your system uses a different suffix for dynamic libraries (e.g. macs use .dylib) then PLUMED will try to
automatically adjust the suffix accordingly.
diff --git a/user-doc/Performances.txt b/user-doc/Performances.txt
index 57bc2c66a554883c04f067b5a2173e32045378a6..00fc973acca246bc871164c6f777ee7e8008cc6e 100644
--- a/user-doc/Performances.txt
+++ b/user-doc/Performances.txt
@@ -105,12 +105,12 @@ a factor equal to STRIDE.
This technique can allow your simulation to run faster if you need
the apply a bias potential on some very expensive collective variable.
Consider the following input:
-\verbatim
+\plumedfile
c1: COM ATOMS=1-1000
c2: COM ATOMS=1001-2000
d: DISTANCE ATOMS=c1,c2
METAD ARG=d HEIGHT=1 SIGMA=0.1 BIASFACTOR=5 PACE=500
-\endverbatim
+\endplumedfile
This performs a \ref METAD simulation biasing the distance between two
centers of mass. Since computing these centers requires a lot of atoms
to be imported from the MD engine, it could slow down significantly the
@@ -118,12 +118,12 @@ simulation. Notice that whereas the bias is changed every PACE=500 steps,
it is applied every STRIDE step, where STRIDE=1 by default.
The following input could lead to a significantly faster simulation at the price
of a negligible systematic error
-\verbatim
+\plumedfile
c1: COM ATOMS=1-1000
c2: COM ATOMS=1001-2000
d: DISTANCE ATOMS=c1,c2
METAD ARG=d HEIGHT=1 SIGMA=0.1 BIASFACTOR=5 PACE=500 STRIDE=2
-\endverbatim
+\endplumedfile
Similarly, the STRIDE keyword can be used with other biases (e.g. \ref RESTRAINT).
The technique is discussed in details here \cite Ferrarotti2015.
@@ -133,9 +133,9 @@ See also \subpage EFFECTIVE_ENERGY_DRIFT.
Whenever you have a multicolvar action such as:
-\verbatim
+\plumedfile
COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=1. D_MAX=3.0} MORE_THAN={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0}
-\endverbatim
+\endplumedfile
You will get a collosal speedup by specifying the D_MAX keyword in all switching functions that act on distances.
D_MAX tells PLUMED that the switching function is strictly zero if the distance is greater than this value. As a result
diff --git a/user-doc/Regex.txt b/user-doc/Regex.txt
index b24524a0f8424daa1a03ab3853efe475f18549fa..93561f632200703b840f5a97f9f5530691341fdb 100644
--- a/user-doc/Regex.txt
+++ b/user-doc/Regex.txt
@@ -14,14 +14,14 @@ Regular expressions are enclosed in round braces and must not contain spaces (th
names have no spaces indeed, so why use them?).
As an example then command
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2 COMPONENTS
PRINT ARG=(d1\.[xy]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
will cause both the d1.x and d1.y components of the DISTANCE action to be printed out in the order that they are created by plumed.
The "." character must be escaped in order to interpret it as a literal ".". An unescaped dot is a wildcard which is matched by any character,
So as an example
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2 COMPONENTS
dxy: DISTANCE ATOMS=1,3
@@ -30,26 +30,26 @@ PRINT ARG=(d1.[xy]) STRIDE=100 FILE=colvar FMT=%8.4f
# while this will match d1.x,d1.y only
PRINT ARG=(d1\.[xy]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
You can include more than one regular expression by using comma separated regular expressions
-\verbatim
+\plumedfile
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1\.[xy]),(t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
(this selects t1,t2,d1.x and d2.x) Be aware that if you have overlapping selection they will be duplicated so it
a better alternative is to use the "or" operator "|".
-\verbatim
+\plumedfile
t1: TORSION ATOMS=5,7,9,15
t2: TORSION ATOMS=7,9,15,17
d1: DISTANCE ATOMS=7,17 COMPONENTS
PRINT ARG=(d1\.[xy]|t[0-9]) STRIDE=100 FILE=colvar FMT=%8.4f
-\endverbatim
+\endplumedfile
this selects the same set of arguments as the previous example.
diff --git a/user-doc/Syntax.txt b/user-doc/Syntax.txt
index 47c73c1f2f6066f5bc66a2e5e6a282e57baee995..277d339e9e98234513d0177008319d53701c42a8 100644
--- a/user-doc/Syntax.txt
+++ b/user-doc/Syntax.txt
@@ -25,18 +25,16 @@ is enclosed in curly braces (e.g. ATOMS={1 2 3 4}). Please note that you can sp
The most important of these keywords is the label keyword as it is only by using these labels that we can pass data
from one action to another. As an example if you do:
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,2
-\endverbatim
-(see \ref DISTANCE)
+\endplumedfile
Then PLUMED will do nothing other than read in your input file. In contrast if you do:
-\verbatim
+\plumedfile
DISTANCE ATOMS=1,2 LABEL=d1
PRINT ARG=d1 FILE=colvar STRIDE=10
-\endverbatim
-(see \ref PRINT)
+\endplumedfile
then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
PLUMED to take the value calculated by the action d1 and to print it. You can use any character string to label your actions
@@ -46,10 +44,10 @@ code-generated groups of atoms and to give labels to any Actions for which the u
Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically
removes it and adds an equivalent label (LABEL=pippo).
Thus, a completely equivalent result can be obtained with the following shortcut:
-\verbatim
+\plumedfile
d1: DISTANCE ATOMS=1,2
PRINT ARG=d1 FILE=colvar STRIDE=10
-\endverbatim
+\endplumedfile
Also notice that all the actions can be labeled, and that many actions besides normal collective variables can define
one or more value, which can be then referred using the corresponding label.
diff --git a/user-doc/go-doxygen b/user-doc/go-doxygen
index aff6debd19910bff68444c93607381c42a462212..a3d87e2011b130f48246935f1617d58980cec54a 100755
--- a/user-doc/go-doxygen
+++ b/user-doc/go-doxygen
@@ -36,7 +36,8 @@ awk -v version="$version" '{
print " <li><a href=\"tutorials.html\"><span>Tutorials</span></a></li>"
print " <li><a href=\"glossary.html\"><span>Index of Actions</span></a></li>"
} else print
-}' $file > $file.tmp
+}' $file |
+awk -f plumed-syntax.awk > $file.tmp
mv $file.tmp $file
done
# end of DOXYGEN <=1.8.10
@@ -51,7 +52,6 @@ var menudata={children:[
EOF
# end of DOXYGEN >=1.8.12
-
cat html/doxygen.css plumed.css > html/doxygen.css.tmp
mv html/doxygen.css.tmp html/doxygen.css
diff --git a/user-doc/plumed-syntax.awk b/user-doc/plumed-syntax.awk
new file mode 100755
index 0000000000000000000000000000000000000000..7d261bca4f246755b1fed2af9d3650a1508f5b93
--- /dev/null
+++ b/user-doc/plumed-syntax.awk
@@ -0,0 +1,54 @@
+{
+ if(match($0,"BEGIN_PLUMED_FILE")){
+ inside=1;
+ sub("BEGIN_PLUMED_FILE","");
+ print;
+ next;
+ }
+ if(inside && match($0,"</pre>")){
+ inside=0;
+ print;
+ next;
+ }
+ if(!inside){
+ print;
+ next;
+ }
+
+# DRAFT LINK TO DOC:
+ copy=$0
+ sub("#.*","",copy);
+ nw=split(copy,words);
+ if(match(words[1],".*:$")){
+ action=words[2];
+ } else {
+ action=words[1];
+ }
+ if(action=="__FILL__") action=""
+ actionx="";
+ for(i=1;i<=length(action);i++){
+ letter=substr(action,i,1);
+ if(match(letter,"[A-Z]")) letter = "_" tolower(letter);
+ actionx=actionx letter;
+ }
+ if(incontinuation) action="";
+ if(incontinuation && words[1]=="...") incontinuation=0;
+ else if(!incontinuation && words[nw]=="...") incontinuation=1;
+
+ if(length(action)>0){
+ actionfile="html/" actionx ".html";
+ if(getline tmp < actionfile < 0) print "WARNING: file " actionfile " does not exist" > "/dev/stderr";
+ else {
+ p=match($0,action);
+ $0=substr($0,1,p-1) "<a href=\"./" actionx ".html\" style=\"color:green\">" action "</a>" substr($0,p+length(action));
+ }
+ }
+
+ gsub("__FILL__","<span style=\"background-color:yellow\">__FILL__</span>");
+
+# comments:
+# sub("#","<span style=\"color:blue\">#");
+# if(match($0,"span style=")) $0=$0 "</span>";
+ sub("#.*$","<span style=\"color:blue\">&</span>");
+ print
+}