diff --git a/developer-doc/usingDoxygen.md b/developer-doc/usingDoxygen.md
index e0dda8b7d3241d65125246cf6dfcf063a45826bc..ea4dd53528510a35e85d08cbb6d73c8febf594da 100644
--- a/developer-doc/usingDoxygen.md
+++ b/developer-doc/usingDoxygen.md
@@ -478,7 +478,25 @@ checks the input will complain.
\subsection molfileeg Using MOLFILE in your example input files
-To be written
+If you use have used a \ref MOLINFO command in the example input that you specified as has been done here:
+
+<pre class="fragment">
+<a href="./_m_o_l_i_n_f_o.html" style="color:green">MOLINFO</a> STRUCTURE=helix.pdb
+<a href="./_w_h_o_l_e_m_o_l_e_c_u_l_e_s.html" style="color:green">WHOLEMOLECULES</a> ENTITY0=1-100
+alpha: <a href="./_a_l_p_h_a_r_m_s_d.html" style="color:green">ALPHARMSD</a> RESIDUES=all TYPE=OPTIMAL R_0=0.1
+</pre>
+
+Then you must provide information on the location from whence PLUMED can the reference input so that the example checking script can copy the input
+for the MOLINFO. The above input would thus be included in the manual as shown below:
+
+\verbatim
+\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
+MOLINFO STRUCTURE=helix.pdb
+WHOLEMOLECULES ENTITY0=1-100
+alpha: ALPHARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1
+\ endplumedfile /*** But with no space between the \ and the endplumedfile
+\endverbatim
\section tutorials Writing how-to instructions
diff --git a/src/colvar/EEFSolv.cpp b/src/colvar/EEFSolv.cpp
index c5fd6dbc72b64ba9068181359a73f550fc56dc97..58d2ca69ac47e8be74f465b62f13681cb63123b4 100644
--- a/src/colvar/EEFSolv.cpp
+++ b/src/colvar/EEFSolv.cpp
@@ -59,6 +59,7 @@ The output from this collective variable, the free energy of solvation, can be u
\par Examples
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
WHOLEMOLECULES ENTITY0=1-111
diff --git a/src/colvar/ERMSD.cpp b/src/colvar/ERMSD.cpp
index 42f03a4025b28443136c8c6855af0e8fe4778ea4..ad0e175d66a571b480127c57c75897000ce102fe 100644
--- a/src/colvar/ERMSD.cpp
+++ b/src/colvar/ERMSD.cpp
@@ -94,6 +94,7 @@ Calculate the eRMSD from reference structure reference.pdb using the default cut
considering residues 1,2,3,4,5,6.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt-ermsd/ref.pdb
MOLINFO STRUCTURE=reference.pdb
eRMSD1: ERMSD REFERENCE=reference.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6
\endplumedfile
diff --git a/src/colvar/Puckering.cpp b/src/colvar/Puckering.cpp
index 62b3158352ea6ee9d7ee9537fd47903c5512cc92..a68bd25255bbaf8aa7325e7fae4069f91dc52a64 100644
--- a/src/colvar/Puckering.cpp
+++ b/src/colvar/Puckering.cpp
@@ -65,6 +65,7 @@ namespace colvar {
This input tells plumed to print the puckering phase angle of the 3rd nucleotide of a RNA molecule on file COLVAR.
\plumedfile
+ #SETTINGS MOLFILE=regtest/basic/rt65/AA.pdb
MOLINFO STRUCTURE=rna.pdb MOLTYPE=rna
PUCKERING ATOMS=@sugar-3 LABEL=puck
PRINT ARG=puck.phs FILE=COLVAR
diff --git a/src/colvar/Torsion.cpp b/src/colvar/Torsion.cpp
index 9c0c0ddbee748714d8243b4d6ca9c4c03c69efff..7d0954e43c4f397fb985cc04db6a89a49a9440d6 100644
--- a/src/colvar/Torsion.cpp
+++ b/src/colvar/Torsion.cpp
@@ -55,6 +55,7 @@ by using TORSION in combination with the \ref MOLINFO command. This can be done
syntax.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
diff --git a/src/generic/DumpAtoms.cpp b/src/generic/DumpAtoms.cpp
index 0a08259ca429d8b145bcb14c40cc6a9989844a26..6bad49b339ff220a254f2a7beee4ffd2b8e08bcd 100644
--- a/src/generic/DumpAtoms.cpp
+++ b/src/generic/DumpAtoms.cpp
@@ -88,6 +88,7 @@ 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.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
# this is required to have proper atom names:
MOLINFO STRUCTURE=reference.pdb
# if omitted, atoms will have "X" name...
diff --git a/src/generic/WholeMolecules.cpp b/src/generic/WholeMolecules.cpp
index 1ead3d79189be79a0662a50f2b5d5c055b5af2a9..33843bd7308e3f4fd8e57973d1beee32501be099 100644
--- a/src/generic/WholeMolecules.cpp
+++ b/src/generic/WholeMolecules.cpp
@@ -91,6 +91,7 @@ This command instructs plumed to reconstruct the chain of backbone atoms in a
protein
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES RESIDUES=all MOLTYPE=protein
\endplumedfile
diff --git a/src/isdb/Jcoupling.cpp b/src/isdb/Jcoupling.cpp
index 46a02f155c7b65affd6cc324a21527267c4058b7..48e3f8d98bc6fabb124e36b1896169584441362f 100644
--- a/src/isdb/Jcoupling.cpp
+++ b/src/isdb/Jcoupling.cpp
@@ -64,7 +64,7 @@ dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental
the correlation and other measures and finally print the results.
\plumedfile
-
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb
WHOLEMOLECULES ENTITY0=1-111
diff --git a/src/multicolvar/AlphaBeta.cpp b/src/multicolvar/AlphaBeta.cpp
index 75006b4f823d919382844e3c82b6978f99b6348b..c8056eebf14b4d731d9f4ec06aea84479d5fec89 100644
--- a/src/multicolvar/AlphaBeta.cpp
+++ b/src/multicolvar/AlphaBeta.cpp
@@ -76,6 +76,7 @@ can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
ALPHABETA ...
ATOMS1=@phi-3 REFERENCE=3.14
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
index 4460d24913073cdd9e97a0d4c426e2a82195caac..e4d48273bf7aa6aefef98b5e4fd411019d151dc4 100644
--- a/src/multicolvar/DihedralCorrelation.cpp
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -66,6 +66,7 @@ can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
dih: DIHCOR ...
ATOMS1=@phi-3,@psi-3
diff --git a/src/multicolvar/Torsions.cpp b/src/multicolvar/Torsions.cpp
index 13889c1a1385a4b8709e5cb27c6f7cb99af1a9f7..14f3775433ece589da91f21a88f4c6cf285564b9 100644
--- a/src/multicolvar/Torsions.cpp
+++ b/src/multicolvar/Torsions.cpp
@@ -56,6 +56,7 @@ can avoid this by using the \ref MOLINFO command. PLUMED uses the pdb file that
about the topology of the protein molecule. This means that you can specify torsion angles using the following syntax:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
TORSIONS ...
ATOMS1=@phi-3
diff --git a/src/pamm/PAMM.cpp b/src/pamm/PAMM.cpp
index 7e847bc5fbb0777fd2e07ca5263b919558f889b7..259f5d543937ead29044ccede664c83ef0a8597e 100644
--- a/src/pamm/PAMM.cpp
+++ b/src/pamm/PAMM.cpp
@@ -60,6 +60,7 @@ looking through the example given below.
In this example I will explain in detail what the following input is computing:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=M1d.pdb
psi: TORSIONS ATOMS1=@psi-2 ATOMS2=@psi-3 ATOMS3=@psi-4
phi: TORSIONS ATOMS1=@phi-2 ATOMS2=@phi-3 ATOMS3=@phi-4
diff --git a/src/secondarystructure/AlphaRMSD.cpp b/src/secondarystructure/AlphaRMSD.cpp
index af672a28d986d72f0494dd8a29d5b40dd1f3c70e..b0c2e2b2b8221e41e0f7114ccdc0b993443f44e8 100644
--- a/src/secondarystructure/AlphaRMSD.cpp
+++ b/src/secondarystructure/AlphaRMSD.cpp
@@ -68,6 +68,7 @@ The following input calculates the number of six residue segments of
protein that are in an alpha helical configuration.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=helix.pdb
alpha: ALPHARMSD RESIDUES=all
\endplumedfile
@@ -75,6 +76,7 @@ alpha: ALPHARMSD RESIDUES=all
Here the same is done use RMSD instead of DRMSD
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES ENTITY0=1-100
alpha: ALPHARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index 814ca6a98b1f2848cb6644ded8df0e3a5d3b7f7b..0bd676124fab7dd724217e916fedaf8cb5a9a117 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -70,6 +70,7 @@ The following input calculates the number of six residue segments of
protein that are in an antiparallel beta sheet configuration.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=beta.pdb
ab: ANTIBETARMSD RESIDUES=all STRANDS_CUTOFF=1
\endplumedfile
@@ -77,6 +78,7 @@ ab: ANTIBETARMSD RESIDUES=all STRANDS_CUTOFF=1
Here the same is done use RMSD instead of DRMSD
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES ENTITY0=1-100
hh: ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1 STRANDS_CUTOFF=1
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index a781278e961f73656121cb523bdfe52e51a87438..c93237eb74b89077bd5ce591a1899d44e3787e42 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -70,6 +70,7 @@ The following input calculates the number of six residue segments of
protein that are in an parallel beta sheet configuration.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=beta.pdb
pb: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1
\endplumedfile
@@ -77,6 +78,7 @@ pb: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1
Here the same is done use RMSD instead of DRMSD
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=helix.pdb
WHOLEMOLECULES ENTITY0=1-100
hh: PARABETARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1 STRANDS_CUTOFF=1
diff --git a/src/setup/MolInfo.cpp b/src/setup/MolInfo.cpp
index 1ad655d1ecf79f6afb958bef29d77b1052dec079..8189a9d4596d01ff5138374059adad53993aacc9 100644
--- a/src/setup/MolInfo.cpp
+++ b/src/setup/MolInfo.cpp
@@ -160,6 +160,7 @@ In the following example the MOLINFO command is used to provide the information
are in the backbone of a protein to the ALPHARMSD CV.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=reference.pdb
ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
\endplumedfile
@@ -168,6 +169,7 @@ The following example prints the distance corresponding to the hydrogen bonds
in a GC Watson-Crick pair.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt-ermsd/ref.pdb
MOLINFO STRUCTURE=reference.pdb MOLTYPE=dna
hb1: DISTANCE ATOMS=@N2-2,@O2-15
hb2: DISTANCE ATOMS=@N1-2,@N3-15
@@ -178,6 +180,7 @@ PRINT ARG=hb1,hb2,hb3
This example use MOLINFO to calculate torsion angles
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
t1: TORSION ATOMS=@phi-3
t2: TORSION ATOMS=@psi-4
diff --git a/user-doc/Miscelaneous.md b/user-doc/Miscelaneous.md
index 01e9712f20287eb0c5e505dac68e3b196341a46b..a743ae6a70ed0994b7fdf023f5ddc63b865dbb8d 100644
--- a/user-doc/Miscelaneous.md
+++ b/user-doc/Miscelaneous.md
@@ -643,6 +643,7 @@ You might have noticed that from time to time constants are specified using stri
An example is the following
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt65/AA.pdb
MOLINFO STRUCTURE=AA.pdb MOLTYPE=rna
e1: TORSION ATOMS=@epsilon-1
t: METAD ARG=e1 SIGMA=0.15 PACE=10 HEIGHT=2 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=200
@@ -654,6 +655,7 @@ as `0.5pi` and `-pi`. However, as of version 2.4, we use the Lepton library in o
that we read. This means that you can also employ more complicated expressions such as `1+2` or `exp(10)`:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt65/AA.pdb
MOLINFO STRUCTURE=AA.pdb MOLTYPE=rna
e1: TORSION ATOMS=@epsilon-1
RESTRAINT ARG=e1 AT=1+0.5
diff --git a/user-doc/go-example-check b/user-doc/go-example-check
index 846bedfdf60e469779631860a0a66d9533a48928..462cb8501778e4c837b3ea8c372d1b7a7ddb4c38 100755
--- a/user-doc/go-example-check
+++ b/user-doc/go-example-check
@@ -5,7 +5,7 @@ mkdir example-check
# This generates plumed.dat files for each of the documentation pages in the manual
for file in *PP.md automatic/*.txt ../CHANGES/*.md tutorials/*.txt tutorials/*.site tutorials/others/*.txt ; do
- #echo Generating examples to check for file $file
+ # echo Generating examples to check for file $file
# Single replica examples
splits=`echo $file | sed -e 's/\// /g'`
nf=`echo $splits | awk '{print NF}'`
@@ -97,19 +97,14 @@ for dir in * ; do
molfile=`grep "MOLINFO" $file | wc -l | awk '{print $1}'`
nfill=`grep "__FILL__" $file | wc -l | awk '{print $1}'`
if [ $molfile -gt 0 ] && [ $nfill -eq 0 ] ; then
- hasermds=`grep "ERMSD" $file | wc -l | awk '{print $1}'`
- isdna=`grep "MOLTYPE=dna" $file | wc -l | awk '{print $1}'`
- isrna=`grep "MOLTYPE=rna" $file | wc -l | awk '{print $1}'`
- inpf=`grep "STRUCTURE=" $file | awk '{for(i=1;i<=NF;++i){ if($i ~ /STRUCTURE=/){ print $i; }}}' | sed -e 's/STRUCTURE=//'`
- if [ $hasermds -gt 0 ] ; then
- cp ../../../regtest/basic/rt-ermsd/ref.pdb $inpf
- elif [ $isdna -gt 0 ] ; then
- cp ../../../regtest/basic/rt-ermsd/ref.pdb $inpf
- elif [ $isrna -gt 0 ] ; then
- cp ../../../regtest/basic/rt65/AA.pdb $inpf
- else
- cp ../../../regtest/basic/rt32/helix.pdb $inpf
+ hasmol=`grep "#SETTINGS" $file | grep "MOLFILE=" | wc -l | awk '{print $1}'`
+ if [ $hasmol -eq 0 ] ; then
+ echo For example $file in $dir you need to include a MOLFILE= keyword in the SETTINGS line
+ exit 1
fi
+ molname=`grep "#SETTINGS" $file | awk '{for(i=1;i<=NF;++i){if(match($i,"MOLFILE=")){print $i}}}' | sed -e 's/MOLFILE=//'`
+ inpf=`grep "STRUCTURE=" $file | awk '{for(i=1;i<=NF;++i){ if($i ~ /STRUCTURE=/){ print $i; }}}' | sed -e 's/STRUCTURE=//'`
+ cp ../../../$molname $inpf
fi
# Now running test with PLUMED
diff --git a/user-doc/tutorials/a-trieste-3.txt b/user-doc/tutorials/a-trieste-3.txt
index dac69051b37e0d26f434ae8fada83230356a6413..816db7a03d38a85a1db63dfec828b14dcd71a730 100644
--- a/user-doc/tutorials/a-trieste-3.txt
+++ b/user-doc/tutorials/a-trieste-3.txt
@@ -384,6 +384,7 @@ gnuplot and add a bias using an analytical function of a collective variable wit
As a first test lets run an MD and generate on-the-fly the free energy as a function of the phi and psi collective variables separately.
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/trieste-3/aladip/aladip.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=aladip.pdb
phi: TORSION ATOMS=@phi-2
@@ -417,6 +418,7 @@ The function and the resulting parameters can be used to run a new biased simula
\section trieste-3-ex-7 Exercise 7: First biased run with Alanine dipeptide
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/trieste-3/aladip/aladip.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=aladip.pdb
@@ -448,6 +450,7 @@ We can now run a third simulation where both regions are biased.
\section trieste-3-ex-8 Exercise 8: Second biased run with Alanine dipeptide
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/trieste-3/aladip/aladip.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=aladip.pdb
@@ -473,6 +476,7 @@ With this third simulation it should be possible to visit both regions as a func
and obtain a better free energy estimate along phi.
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/trieste-3/aladip/aladip.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=aladip.pdb
diff --git a/user-doc/tutorials/a-trieste-6.txt b/user-doc/tutorials/a-trieste-6.txt
index 2ef9d4dd78eefbbf6cff31ceac844a389a996732..513b25a5119834bfb0017a08fa6774d868e528b4 100644
--- a/user-doc/tutorials/a-trieste-6.txt
+++ b/user-doc/tutorials/a-trieste-6.txt
@@ -195,6 +195,7 @@ The users should select two of them for the \ref METAD simulation. Once you are
to evaluate the free-energy difference between folded and unfolded state as a function of multiple collective variables.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
#this allows you to use short-cut for dihedral angles
MOLINFO STRUCTURE=GB1_native.pdb
diff --git a/user-doc/tutorials/aa-lugano-2.txt b/user-doc/tutorials/aa-lugano-2.txt
index 4c92988a1e994766457499de18e66a6a275ccd8a..28438c3b5dbe26de5d0016dff38981c0fc89653c 100644
--- a/user-doc/tutorials/aa-lugano-2.txt
+++ b/user-doc/tutorials/aa-lugano-2.txt
@@ -121,6 +121,7 @@ As a first test lets run an MD and generate on-the-fly the free energy as a func
This is an example input file to calculate the phi and psi angles on the fly and accumulate two 1D histograms from which calculating the free energy.
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/lugano-2/diala.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=diala.pdb
phi: TORSION ATOMS=@phi-2
@@ -178,6 +179,7 @@ The function and the resulting parameters can be used to run a new biased simula
To the above file we add a few lines to define using \ref CUSTOM a function of the angle phi.
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/lugano-2/diala.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=diala.pdb
phi: TORSION ATOMS=@phi-2
@@ -217,6 +219,7 @@ We can now run a third simulation where both regions are biased.
\section lugano-2-ex-3 Exercise 3: Second biased run with alanine dipeptide
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/lugano-2/diala.pdb
MOLINFO STRUCTURE=diala.pdb
phi: TORSION ATOMS=@phi-2
psi: TORSION ATOMS=@psi-2
@@ -244,6 +247,7 @@ is flatter than the former even if not flat everywhere. Now it is possible to re
and obtain a better free energy estimate along phi.
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/lugano-2/diala.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=diala.pdb
@@ -328,6 +332,7 @@ gmx trjcat -f traj*.xtc -cat -o concatenated.xtc
2) calculate the values for all employed biases applied on each frame
for this we can write a plumed-wham.dat file including all the biases used in the former simulations:
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/lugano-2/diala.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=diala.pdb
phi: TORSION ATOMS=@phi-2
@@ -391,7 +396,7 @@ is presented in the following but the exercise is possible only if plumed is com
Here we use the "replica" syntax of plumed to write a single plumed input file for all the windows:
\plumedfile
-#SETTINGS FILENAME=plumed.dat
+#SETTINGS FILENAME=plumed.dat MOLFILE=user-doc/tutorials/lugano-2/diala.pdb
# this is plumed.dat
# vim:ft=plumed
MOLINFO STRUCTURE=diala.pdb
diff --git a/user-doc/tutorials/aa-lugano-6d.txt b/user-doc/tutorials/aa-lugano-6d.txt
index d56f45581e9d0df145e489be1fbf9a75118c53a7..b517d10c01e64bd106fe608373b6343a94ab7dc1 100644
--- a/user-doc/tutorials/aa-lugano-6d.txt
+++ b/user-doc/tutorials/aa-lugano-6d.txt
@@ -61,6 +61,7 @@ Once you are satisfied by the convergence of your simulation, you can use one of
to evaluate the free-energy difference between folded and unfolded state as a function of multiple collective variables.
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/lugano-6d/GB1_native.pdb
#this allows you to use short-cut for dihedral angles
MOLINFO STRUCTURE=GB1_native.pdb
diff --git a/user-doc/tutorials/marvel-1.txt b/user-doc/tutorials/marvel-1.txt
index b960a3a0a0ed9ecdeceec98cb79f75c5c1729ea4..68673abbd7a5beb002b12c59bf9e1bb830c6e7c6 100644
--- a/user-doc/tutorials/marvel-1.txt
+++ b/user-doc/tutorials/marvel-1.txt
@@ -277,6 +277,7 @@ angles). The \ref MOLINFO command makes it particularly easy to do this. For i
in the sixth residue of the protein and the \f$\psi\f$ angle in the eighth residue of the protein. You can do so using the following input:
\verbatim
+#SETTINGS MOLFILE=user-doc/tutorials/marvel-1/template.pdb
MOLINFO STRUCTURE=template.pdb
phi6: TORSION ATOMS=@phi-6
psi8: TORSION ATOMS=@psi-8
@@ -360,6 +361,7 @@ below to calculate the degree of anti-beta secondary structure in each of the tr
and by exploiting the commands to run driver that were described in section \ref marvel-1-introinput.
\verbatim
+#SETTINGS MOLFILE=user-doc/tutorials/marvel-1/template.pdb
MOLINFO STRUCTURE=template.pdb
abeta: ANTIBETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} STRANDS_CUTOFF=1
@@ -564,6 +566,7 @@ We are going to calculate the \ref HISTOGRAM from our protein trajectory as a fu
calculate perform this analysis is shown below:
\verbatim
+#SETTINGS MOLFILE=user-doc/tutorials/marvel-1/template.pdb
# Read in protein structure template
MOLINFO STRUCTURE=template.pdb
# Calculate collective variables
@@ -599,6 +602,7 @@ F(s) = -k_B T \ln H(s)
If you want to use PLUMED to output the free energy rather than the histogram you need to use the \ref CONVERT_TO_FES command as shown below:
\verbatim
+#SETTINGS MOLFILE=user-doc/tutorials/marvel-1/template.pdb
# Read in protein structure template
MOLINFO STRUCTURE=template.pdb
# Calculate collective variables
diff --git a/user-doc/tutorials/munster.txt b/user-doc/tutorials/munster.txt
index bef53426ee78e2217490e478c780a080754f9e2a..7f7f5f09aa35032dfaaac6a89f8fd9a9cb1b5600 100644
--- a/user-doc/tutorials/munster.txt
+++ b/user-doc/tutorials/munster.txt
@@ -248,6 +248,7 @@ the atomic positions. This is a very good way to understand what \ref WHOLEMOLEC
is actually doing. Try the following input
\plumedfile
+#SETTINGS MOLFILE=user-doc/tutorials/munster/TOPO/reference.pdb
MOLINFO STRUCTURE=reference.pdb
DUMPATOMS FILE=test1.gro ATOMS=1-22
WHOLEMOLECULES ENTITY0=1-22
diff --git a/user-doc/tutorials/performance-optimization.txt b/user-doc/tutorials/performance-optimization.txt
index 804f9b0215d4bb02423602e58076c51a2715b95f..b2e94cd7944797f3b604c6011e7e6093cb9e4349 100644
--- a/user-doc/tutorials/performance-optimization.txt
+++ b/user-doc/tutorials/performance-optimization.txt
@@ -51,6 +51,7 @@ Scaling is approximately linear.
Now you can run GROMACS with PLUMED using the following input file
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=conf.pdb
# @water and @hydrogens are special groups introduce in PLUMED 2.5!
wat: GROUP ATOMS=@water
@@ -130,6 +131,7 @@ The recommended procedure is to first perform a simulation where you compute you
For instance:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=conf.pdb
wat: GROUP ATOMS=@water
ow: GROUP ATOMS=@water REMOVE=@hydrogens
@@ -218,6 +220,7 @@ the distance between the magnesium ion and the phosphate. Parameters are similar
although we use here a shorter deposition pace in order to artificially increase the computational cost.
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=conf.pdb
wat: GROUP ATOMS=@water
ow: GROUP ATOMS=@water REMOVE=@hydrogens
@@ -249,6 +252,7 @@ for((i=0;i<=10000;i++)) ; do echo "$var" ; done | awk '{if($1!="#!") print $1,$2
Now modify your `plumed.dat` file so that it will read the `HILLS_long` file:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFO STRUCTURE=conf.pdb
wat: GROUP ATOMS=@water
ow: GROUP ATOMS=@water REMOVE=@hydrogens
@@ -289,6 +293,7 @@ Let's see what happens using the GPU. In this case the first couple of thousands
GROMACS tries to optimize the GPU load, so we should run a longer simulation to estimate the simulation speed.
For simplicity, use the following `plumed.dat` file:
\plumedfile
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
# vim:ft=plumed
MOLINFO STRUCTURE=conf.pdb
DEBUG DETAILED_TIMERS