diff --git a/src/adjmat/ClusterDistribution.cpp b/src/adjmat/ClusterDistribution.cpp
index 400fed6112457ab3bd25f45de9882a3dd97b7ea5..a18b73758248a0587753f97edbc42264961b8046 100644
--- a/src/adjmat/ClusterDistribution.cpp
+++ b/src/adjmat/ClusterDistribution.cpp
@@ -41,11 +41,11 @@ value for the local q6 Steinhardt parameter is then computed. A contact matrix
whether atoms atoms \f$i\f$ and \f$j\f$ have a high value for this coordination number and if they are within
3.6 nm of each other. The connected components of this matrix are then found using a depth first clustering
algorithm on the corresponding graph. The number of components in this graph that contain more than 27 atoms is then computed.
-As discussed in \cite tribello-clustering this input was used to analyze the formation of a polycrystal of GeTe from amorphous
+As discussed in \cite tribello-clustering an input similar to this one was used to analyze the formation of a polycrystal of GeTe from amorphous
GeTe.
\plumedfile
-q6: Q6 SPECIES=1-32768 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM
+q6: Q6 SPECIES=1-300 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}
cc: COORDINATIONNUMBER SPECIES=flq6 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
diff --git a/src/adjmat/ContactMatrix.cpp b/src/adjmat/ContactMatrix.cpp
index be825f0c32ec6784f1b78b67dcd02ea0709b9b72..d2a9fe9ad3a9caa8caaade8e342fa0b68b92a4fb 100644
--- a/src/adjmat/ContactMatrix.cpp
+++ b/src/adjmat/ContactMatrix.cpp
@@ -49,7 +49,7 @@ of each other and which is zero otherwise. The columns in this matrix are then
The final quantity output in the colvar file is thus the average coordination number.
\plumedfile
-aa: CONTACT_MATRIX ATOMS=1-6 SWITCH={EXP D_0=0.2 R_0=0.1 D_MAX=0.66}
+mat: 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
\endplumedfile
diff --git a/src/adjmat/HbondMatrix.cpp b/src/adjmat/HbondMatrix.cpp
index 777f3dd5c92959501299a08d27bca4f5b1ffc30f..f635da2057e01724c9fdfbfadd0830c86688bd13 100644
--- a/src/adjmat/HbondMatrix.cpp
+++ b/src/adjmat/HbondMatrix.cpp
@@ -71,7 +71,7 @@ mat: HBOND_MATRIX ATOMS=1-192:3 HYDROGENS=2-192:3,3-192:3 SWITCH={RATIONAL R_0=3
rsums: ROWSUMS MATRIX=mat MEAN
csums: COLUMNSUMS MATRIX=mat MEAN
DUMPMULTICOLVAR DATA=rsums FILE=donors.xyz
-DUMPMULTICOLVAR DATA=csums FILE=acceptors.x
+DUMPMULTICOLVAR DATA=csums FILE=acceptors.xyz
\endplumedfile
*/
diff --git a/src/adjmat/MatrixRowSums.cpp b/src/adjmat/MatrixRowSums.cpp
index fb60b8b31e25124e906fa25381d41e4412298963..160882d3ed4ae04891f6730ae19866102d2c81dd 100644
--- a/src/adjmat/MatrixRowSums.cpp
+++ b/src/adjmat/MatrixRowSums.cpp
@@ -85,7 +85,7 @@ MatrixRowSums::MatrixRowSums(const ActionOptions& ao):
Action(ao),
ActionWithInputMatrix(ao)
{
- if( (mymatrix->getMatrixAction())->mybasemulticolvars.size()>0 ) error("matrix row sums should only be calculated when inputs are atoms");
+ if( (mymatrix->getMatrixAction())->mybasemulticolvars.size()>0 ) warning("matrix row may be problematic when inputs are not atoms");
// Setup the tasks
unsigned nrows = mymatrix->getNumberOfRows();
ablocks.resize(1); ablocks[0].resize( nrows );
diff --git a/src/adjmat/SMACMatrix.cpp b/src/adjmat/SMACMatrix.cpp
index 617abcdb35139639a76fd1a1a6712b7bd3070521..26e0819933fa521b0c4f279561cb451e18e5a596 100644
--- a/src/adjmat/SMACMatrix.cpp
+++ b/src/adjmat/SMACMatrix.cpp
@@ -64,12 +64,12 @@ LABEL=m1
SMAC_MATRIX ...
ATOMS=m1 SWITCH={RATIONAL D_0=5.99 R_0=0.1 D_MAX=6.0}
KERNEL1={TRIANGULAR CENTER=0 SIGMA=1.0} KERNEL2={TRIANGULAR CENTER=pi SIGMA=0.6}
- LABEL=smacm
+ LABEL=smac
... SMAC_MATRIX
-dfs1: DFSCLUSTERING MATRIX=smacm
+dfs1: DFSCLUSTERING MATRIX=smac
cc2: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1
-PRINT ARG=smac.*,cc1.*,cc2 FILE=colvar
+PRINT ARG=cc2 FILE=colvar
\endplumedfile
*/
diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp
index 59dc8049f710ad2d9e0799a038468cb5744c56ac..0ccc308526059cf7458ffddae862e9e539617baf 100644
--- a/src/analysis/Histogram.cpp
+++ b/src/analysis/Histogram.cpp
@@ -186,7 +186,6 @@ HISTOGRAM ...
GRID_MAX=3.14,3.14
GRID_BIN=200,200
BANDWIDTH=0.05,0.05
- GRID_WFILE=histo
LABEL=hh
... HISTOGRAM
diff --git a/src/bias/BiasValue.cpp b/src/bias/BiasValue.cpp
index 3c4839a39457a8701208263dce1f9d4b245cf5aa..f2730a76bdb0fa7c9beb6592c60a63ba53341d96 100644
--- a/src/bias/BiasValue.cpp
+++ b/src/bias/BiasValue.cpp
@@ -46,7 +46,7 @@ It then tells plumed to print the energy of the restraint
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
+PRINT ARG=d1,d2,b.d1_bias,b.d2_bias
\endplumedfile
Another thing one can do is asking one system to follow
@@ -70,7 +70,7 @@ vv1: MATHEVAL ARG=mycos,mysin,cos,sin VAR=mc,ms,c,s FUNC=100*((mc-c)^2+(ms-s)^
# this takes the value calculated with matheval and uses as a bias
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
+PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.vv1_bias STRIDE=1 FILE=colvar FMT=%8.4f
\endplumedfile
*/
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index f21cbfa906791ccf680a5904ee141c895ef63a40..96b0f1c1d56da9072b725594de4d658d23249aed 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -43,17 +43,24 @@ 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.
\plumedfile
DISTANCE ATOMS=3,5 LABEL=d1
-EXTERNAL ARG=d1 FILE=bias.dat LABEL=external
+EXTERNAL ARG=d1 FILE=bias.grid LABEL=external
\endplumedfile
-The header in the file bias.dat should read:
-\verbatim
+The bias.grid will then look something like this:
+\auxfile{bias.grid}
#! FIELDS d1 external.bias der_d1
-#! SET min_d1 0.0
-#! SET max_d1 1.0
-#! SET nbins_d1 100
+#! SET min_d1 1.14
+#! SET max_d1 1.32
+#! SET nbins_d1 6
#! SET periodic_d1 false
-\endverbatim
+ 1.1400 0.0031 0.1101
+ 1.1700 0.0086 0.2842
+ 1.2000 0.0222 0.6648
+ 1.2300 0.0521 1.4068
+ 1.2600 0.1120 2.6873
+ 1.2900 0.2199 4.6183
+ 1.3200 0.3948 7.1055
+\endauxfile
This should then be followed by the value of the potential and its derivative
at 100 equally spaced points along the distance between 0 and 1.
@@ -64,21 +71,32 @@ potential acting on two torsional angles:
\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
+EXTERNAL ARG=t1,t2 FILE=bias2.grid LABEL=ext
\endplumedfile
-The header in the file bias.dat for this calculation would read:
-\verbatim
+The file bias2.grid for this calculation would need to look something like this:
+\auxfile{bias2.grid}
#! FIELDS t1 t2 ext.bias der_t1 der_t2
#! SET min_t1 -pi
-#! SET max_t1 +pi
-#! SET nbins_t1 100
+#! SET max_t1 pi
+#! SET nbins_t1 3
#! SET periodic_t1 true
#! SET min_t2 -pi
-#! SET max_t2 +pi
-#! SET nbins_t2 100
+#! SET max_t2 pi
+#! SET nbins_t2 3
#! SET periodic_t2 true
-\endverbatim
+ -3.141593 -3.141593 0.000000 -0.000000 -0.000000
+ -1.047198 -3.141593 0.000000 0.000000 -0.000000
+ 1.047198 -3.141593 0.000000 -0.000000 -0.000000
+
+ -3.141593 -1.047198 0.000000 -0.000000 0.000000
+ -1.047198 -1.047198 0.007922 0.033185 0.033185
+ 1.047198 -1.047198 0.007922 -0.033185 0.033185
+
+ -3.141593 1.047198 0.000000 -0.000000 -0.000000
+ -1.047198 1.047198 0.007922 0.033185 -0.033185
+ 1.047198 1.047198 0.007922 -0.033185 -0.033185
+\endauxfile
This would be then followed by 100 blocks of data. In the first block of data the
value of t1 (the value in the first column) is kept fixed and the value of
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index c5aa93ee7c8e0196a09784a2b792a6ea0017c3c8..fe975b677623733d9f85573f134552ec1f44ad1d 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -238,6 +238,9 @@ presented in \cite Tiwary_jp504920s as described above.
This is enabled by using the keyword CALC_RCT,
and can be done only if the bias is defined on a grid.
\plumedfile
+phi: TORSION ATOMS=1,2,3,4
+psi: TORSION ATOMS=5,6,7,8
+
METAD ...
LABEL=metad
ARG=phi,psi SIGMA=0.20,0.20 HEIGHT=1.20 BIASFACTOR=5 TEMP=300.0 PACE=500
@@ -322,22 +325,29 @@ DISTANCE ATOMS=3,5 LABEL=d1
METAD ...
LABEL=t1
ARG=d1 SIGMA=0.05 TAU=200 DAMPFACTOR=100 PACE=250
- GRID_MIN=0 GRID_MAX=2 GRID_BIN=200
- TARGET=dist.dat
+ GRID_MIN=1.14 GRID_MAX=1.32 GRID_BIN=6
+ TARGET=dist.grid
... METAD
PRINT ARG=d1,t1.bias STRIDE=100 FILE=COLVAR
\endplumedfile
-The header in the file dist.dat for this calculation would read:
+The file dist.dat for this calculation would read:
-\verbatim
+\auxfile{dist.grid}
#! FIELDS d1 t1.target der_d1
-#! SET min_d1 0
-#! SET max_d1 2
-#! SET nbins_d1 200
+#! SET min_d1 1.14
+#! SET max_d1 1.32
+#! SET nbins_d1 6
#! SET periodic_d1 false
-\endverbatim
+ 1.1400 0.0031 0.1101
+ 1.1700 0.0086 0.2842
+ 1.2000 0.0222 0.6648
+ 1.2300 0.0521 1.4068
+ 1.2600 0.1120 2.6873
+ 1.2900 0.2199 4.6183
+ 1.3200 0.3948 7.1055
+\endauxfile
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.
diff --git a/src/bias/ReweightMetad.cpp b/src/bias/ReweightMetad.cpp
index 013af2bc47d393ff51614dfad7b4fc2ab3407b4d..9b2400c79a3a1762cd418a7dae8ece0766994e91 100644
--- a/src/bias/ReweightMetad.cpp
+++ b/src/bias/ReweightMetad.cpp
@@ -42,7 +42,7 @@ factor and the grid over which we calculate c(t) in the input to the METAD comma
\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
+METAD ARG=x PACE=100 SIGMA=0.1 HEIGHT=1.5 BIASFACTOR=5 GRID_MIN=0 GRID_MAX=10 GRID_BIN=100 CALC_RCT RCT_USTRIDE=50
bias: REWEIGHT_METAD TEMP=300
diff --git a/src/colvar/Constant.cpp b/src/colvar/Constant.cpp
index 3f82c9ab2961cfb74bf354dbde67992038eef99c..64678097f0e0bf2c210c7fa62af0c59313627c38 100644
--- a/src/colvar/Constant.cpp
+++ b/src/colvar/Constant.cpp
@@ -53,7 +53,7 @@ PRINT ARG=sss.2
In case you want to pass a single value you can use VALUE:
\plumedfile
cn: CONSTANT VALUE=1.0
-dis: DISTANCE ATOMS=1
+dis: DISTANCE ATOMS=1,2
sss: SORT ARG=cn,dis
PRINT ARG=sss.1
\endplumedfile
diff --git a/src/colvar/Coordination.cpp b/src/colvar/Coordination.cpp
index 06073e1b26971348e332cc722d70c441042b2fdc..6898b2eb8d10a2acfabf70b92799c7165f047187 100644
--- a/src/colvar/Coordination.cpp
+++ b/src/colvar/Coordination.cpp
@@ -84,7 +84,7 @@ 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
+c2: COMBINE ARG=x COEFFICIENTS=2 PERIODIC=NO
# 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.
diff --git a/src/colvar/DRMSD.cpp b/src/colvar/DRMSD.cpp
index d89a18869bd4bc1728cccfc51668629452833808..003fbc92981c8eaf1fbc658af5d492db49779ce7 100644
--- a/src/colvar/DRMSD.cpp
+++ b/src/colvar/DRMSD.cpp
@@ -67,19 +67,30 @@ position. Only pairs of atoms whose distance in the reference structure is withi
0.1 and 0.8 nm are considered.
\plumedfile
-DRMSD REFERENCE=file.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8
+DRMSD REFERENCE=file1.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8
\endplumedfile
+The reference file is a PDB file that looks like this
+
+\auxfile{file1.pdb}
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+END
+\endauxfile
+
The following tells plumed to calculate a DRMSD value for a pair of molecules.
\plumedfile
-DRMSD REFERENCE=file.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 TYPE=INTER-DRMSD
+DRMSD REFERENCE=file2.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 TYPE=INTER-DRMSD
\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.
-\verbatim
+\auxfile{file2.pdb}
ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
@@ -87,7 +98,7 @@ TER
ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
END
-\endverbatim
+\endauxfile
In this example the INTER-DRMSD type ensures that the set of distances from which the final
quantity is computed involve one atom from each of the two molecules. If this is replaced
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 763895edacb56b5cf1a53e1514d55c51a19e142c..91a453ae916609961f842be9072dac24f0690ac6 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -51,7 +51,7 @@ The following tells plumed to calculate the dipole of the group of atoms contain
the atoms from 1-10 and print it every 5 steps
\plumedfile
d: DIPOLE GROUP=1-10
-PRINT FILE=output STRIDE=5 ARG=5
+PRINT FILE=output STRIDE=5 ARG=d
\endplumedfile
\attention
diff --git a/src/colvar/MultiRMSD.cpp b/src/colvar/MultiRMSD.cpp
index 490d31c845b6360dbf6746e4a671eff6b3803cea..b0ccb9418981b98730cfeb3346e18ccd26f5067a 100644
--- a/src/colvar/MultiRMSD.cpp
+++ b/src/colvar/MultiRMSD.cpp
@@ -71,7 +71,7 @@ configuration. \f$w_i\f$ is an optional weight.
The distances for each of the domains in the above sum can be calculated using the \ref DRMSD or \ref RMSD measures or
using a combination of these distance. The reference configuration is specified in a pdb file like the one below:
-\verbatim
+\auxfile{file1.pdb}
ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 1.00 DIA O
ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 1.00 DIA H
ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 1.00 DIA H
@@ -89,7 +89,7 @@ ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
END
-\endverbatim
+\endauxfile
with the TER keyword being used to separate the various domains in you protein.
@@ -101,7 +101,7 @@ the positions of the atoms in the reference file and their instantaneous
position. The Kearsley algorithm for each of the domains.
\plumedfile
-MULTI-RMSD REFERENCE=file.pdb TYPE=MULTI-OPTIMAL
+MULTI-RMSD REFERENCE=file1.pdb TYPE=MULTI-OPTIMAL
\endplumedfile
The following tells plumed to calculate the RMSD distance between the positions of
@@ -109,7 +109,7 @@ the atoms in the domains of reference the reference structure and their instanta
positions. Here distances are calculated using the \ref DRMSD measure.
\plumedfile
-MULTI-RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
+MULTI-RMSD REFERENCE=file2.pdb TYPE=MULTI-DRMSD
\endplumedfile
in this case it is possible to use the following DRMSD options in the pdb file using the REMARK syntax:
@@ -120,7 +120,7 @@ UPPER_CUTOFF=# only pairs of atoms further than UPPER_CUTOFF are considered in t
\endverbatim
as shown in the following example
-\verbatim
+\auxfile{file2.pdb}
REMARK NOPBC
REMARK LOWER_CUTOFF=0.1
REMARK UPPER_CUTOFF=0.8
@@ -141,7 +141,7 @@ ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
END
-\endverbatim
+\endauxfile
*/
@@ -161,6 +161,28 @@ Just replace \ref MULTI-RMSD with \ref MULTI_RMSD
MULTI_RMSD REFERENCE=file.pdb TYPE=MULTI-DRMSD
\endplumedfile
+and remember to use a pdb file like the one below to define the reference structure
+
+\auxfile{file.pdb}
+ATOM 2 O ALA 2 -0.926 -2.447 -0.497 1.00 1.00 DIA O
+ATOM 4 HNT ALA 2 0.533 -0.396 1.184 1.00 1.00 DIA H
+ATOM 6 HT1 ALA 2 -0.216 -2.590 1.371 1.00 1.00 DIA H
+ATOM 7 HT2 ALA 2 -0.309 -1.255 2.315 1.00 1.00 DIA H
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+TER
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+ATOM 16 HN ALA 2 1.713 1.021 -0.873 1.00 1.00 DIA H
+ATOM 18 HA ALA 2 0.099 -0.774 -2.218 1.00 1.00 DIA H
+ATOM 19 CB ALA 2 2.063 -1.223 -1.276 1.00 1.00 DIA C
+ATOM 20 HB1 ALA 2 2.670 -0.716 -2.057 1.00 1.00 DIA H
+ATOM 21 HB2 ALA 2 2.556 -1.051 -0.295 1.00 1.00 DIA H
+ATOM 22 HB3 ALA 2 2.070 -2.314 -1.490 1.00 1.00 DIA H
+END
+\endauxfile
+
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PCARMSD.cpp b/src/colvar/PCARMSD.cpp
index 63e40eb19c9d43f2cb76d064f1239c8c33f6fbbf..d235a5cda5a5296cbc40463d06f0e646b137fb46 100644
--- a/src/colvar/PCARMSD.cpp
+++ b/src/colvar/PCARMSD.cpp
@@ -63,6 +63,43 @@ PCARMSD AVERAGE=file.pdb EIGENVECTORS=eigenvectors.pdb
\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).
+The reference configuration (file.pdb) will thus be in a file that looks something like this:
+
+\auxfile{file.pdb}
+TITLE Average structure
+MODEL 1
+ATOM 1 CL ALA 1 1.042 -3.070 0.946 1.00 0.00
+ATOM 5 CLP ALA 1 0.416 -2.033 0.132 1.00 0.00
+ATOM 6 OL ALA 1 0.415 -2.082 -0.976 1.00 0.00
+ATOM 7 NL ALA 1 -0.134 -1.045 0.677 1.00 0.00
+ATOM 9 CA ALA 1 -0.774 0.053 0.003 1.00 0.00
+TER
+ENDMDL
+\endauxfile
+
+while the eigenvectors will be in a pdb file (eigenvectors.pdb) that looks something like this:
+
+\auxfile{eigenvectors.pdb}
+TITLE frame t= -1.000
+MODEL 1
+ATOM 1 CL ALA 1 1.194 -2.988 0.724 1.00 0.00
+ATOM 5 CLP ALA 1 -0.996 0.042 0.144 1.00 0.00
+ATOM 6 OL ALA 1 -1.246 -0.178 -0.886 1.00 0.00
+ATOM 7 NL ALA 1 -2.296 0.272 0.934 1.00 0.00
+ATOM 9 CA ALA 1 -0.436 2.292 0.814 1.00 0.00
+TER
+ENDMDL
+TITLE frame t= 0.000
+MODEL 1
+ATOM 1 CL ALA 1 1.042 -3.070 0.946 1.00 0.00
+ATOM 5 CLP ALA 1 -0.774 0.053 0.003 1.00 0.00
+ATOM 6 OL ALA 1 -0.849 -0.166 -1.034 1.00 0.00
+ATOM 7 NL ALA 1 -2.176 0.260 0.563 1.00 0.00
+ATOM 9 CA ALA 1 0.314 1.825 0.962 1.00 0.00
+TER
+ENDMDL
+
+\endauxfile
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PathMSD.cpp b/src/colvar/PathMSD.cpp
index 790ac8ec57c7c5f4c9c516d081e206ea30657d23..e2e776678248a6aee17cb9ba1dd346b921b501ac 100644
--- a/src/colvar/PathMSD.cpp
+++ b/src/colvar/PathMSD.cpp
@@ -62,7 +62,26 @@ note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighbor list parameter (optio
recommended for performance) and states that the neighbor list will be calculated every 4
steps and consider only the closest 8 member to the actual md snapshots.
-In the REFERENCE PDB file the frames must be separated either using END or ENDMDL.
+This input must be accompanied by a REFERENCE PDB file in which the positions of each of the frames are specified
+separated using either END or ENDMDL as shown below:
+
+\auxfile{file.pdb}
+ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
+ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
+ATOM 6 OL ALA 1 -1.177 -0.889 2.401 1.00 1.00
+ATOM 7 NL ALA 1 -1.313 0.341 0.529 1.00 1.00
+END
+ATOM 1 CL ALA 1 -3.175 0.365 2.024 1.00 1.00
+ATOM 5 CLP ALA 1 -1.814 -0.106 1.685 1.00 1.00
+ATOM 6 OL ALA 1 -1.201 -0.849 2.425 1.00 1.00
+ATOM 7 NL ALA 1 -1.296 0.337 0.534 1.00 1.00
+END
+ATOM 1 CL ALA 1 -2.990 0.383 2.277 1.00 1.00
+ATOM 5 CLP ALA 1 -1.664 -0.085 1.831 1.00 1.00
+ATOM 6 OL ALA 1 -0.987 -0.835 2.533 1.00 1.00
+ATOM 7 NL ALA 1 -1.227 0.364 0.646 1.00 1.00
+END
+\endauxfile
\note
The implementation of this collective variable and of \ref PROPERTYMAP
diff --git a/src/colvar/Position.cpp b/src/colvar/Position.cpp
index b06806299d802eea07609044abc38c8b71c88412..d95a9234f6ccad5fe1ea3c343ff5d169bddd784b 100644
--- a/src/colvar/Position.cpp
+++ b/src/colvar/Position.cpp
@@ -61,6 +61,17 @@ p: POSITION ATOM=3
PRINT ARG=p.x,p.y,p.z
\endplumedfile
+The reference position is specified in a pdb file like the one shown below
+
+\auxfile{ref.pdb}
+ATOM 3 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+END
+\endauxfile
+
*/
//+ENDPLUMEDOC
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index a5934134e863fb67083294ccf724eec654846abc..820bff96b5d3ad16f2d537f7827e30a6d1a5ad89 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -60,7 +60,7 @@ periodic image.
\par Examples
\plumedfile
-p3: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4
+p3: PROPERTYMAP REFERENCE=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
\endplumedfile
@@ -72,18 +72,16 @@ In this case the input line instructs plumed to look for two properties X and Y
line of the reference pdb (Note: No spaces from X and = and 1 !!!!).
e.g.
-\verbatim
+\auxfile{allv.pdb}
REMARK X=1 Y=2
ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
-.......
END
REMARK X=2 Y=3
ATOM 1 CL ALA 1 -3.175 0.365 2.024 1.00 1.00
ATOM 5 CLP ALA 1 -1.814 -0.106 1.685 1.00 1.00
-....
END
-\endverbatim
+\endauxfile
\note
The implementation of this collective variable and of \ref PATHMSD
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index 8ec3f2035c985487770f9d859bd21abbd9dd9863..572fe2f5402350ab780e40054387a621d7d472eb 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -149,6 +149,17 @@ position. The Kearsley algorithm is used so this is done optimally.
RMSD REFERENCE=file.pdb TYPE=OPTIMAL
\endplumedfile
+The reference configuration is specified in a pdb file that will have a format similar to the one shown below:
+
+\auxfile{file.pdb}
+ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
+ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
+ATOM 6 OL ALA 1 -1.177 -0.889 2.401 1.00 1.00
+ATOM 7 NL ALA 1 -1.313 0.341 0.529 1.00 1.00
+ATOM 8 HL ALA 1 -1.845 0.961 -0.011 1.00 1.00
+END
+\endauxfile
+
...
*/
diff --git a/src/crystallization/MoleculeOrientation.cpp b/src/crystallization/MoleculeOrientation.cpp
index 8112b9a563691bac74212a38b6a939aa1ccbafeb..a2ed7f598be906a64c259092e288a02e2c338737 100644
--- a/src/crystallization/MoleculeOrientation.cpp
+++ b/src/crystallization/MoleculeOrientation.cpp
@@ -64,7 +64,7 @@ public:
PLUMED_REGISTER_ACTION(MoleculeOrientation,"MOLECULES")
void MoleculeOrientation::registerKeywords( Keywords& keys ) {
- VectorMultiColvar::registerKeywords( keys ); keys.use("VMEAN");
+ VectorMultiColvar::registerKeywords( keys ); keys.use("MEAN"); keys.use("VMEAN");
keys.add("numbered","MOL","The numerical indices of the atoms in the molecule. The orientation of the molecule is equal to "
"the vector connecting the first two atoms specified. If a third atom is specified its position "
"is used to specify where the molecule is. If a third atom is not present the molecule is assumed "
diff --git a/src/crystallization/Q6.cpp b/src/crystallization/Q6.cpp
index a784607b1162306bdb0837db8c55dbdd29ffeacc..f9729b48a3212b2681b4a84ac16c5353fcd90451 100644
--- a/src/crystallization/Q6.cpp
+++ b/src/crystallization/Q6.cpp
@@ -156,7 +156,7 @@ are done with those of all the other atoms in the system. The final quantity is
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 SPECIES=q4a,q4b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w4
+LOCAL_Q6 SPECIES=q6a,q6b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w6
PRINT ARG=w6.* FILE=colvar
\endplumedfile
diff --git a/src/dimred/ClassicalMultiDimensionalScaling.cpp b/src/dimred/ClassicalMultiDimensionalScaling.cpp
index af8ab1e62522e1693603ccd2ffe93e064955fe93..c9b07a2a636fc1ec43b64b75e858eaadc8ed37eb 100644
--- a/src/dimred/ClassicalMultiDimensionalScaling.cpp
+++ b/src/dimred/ClassicalMultiDimensionalScaling.cpp
@@ -51,12 +51,10 @@ The following command instructs plumed to construct a classical multidimensional
The RMSD distance between atoms 1-256 have moved is used to measure the distances in the high-dimensional space.
\plumedfile
-CLASSICAL_MDS ...
- ATOMS=1-256
- METRIC=OPTIMAL-FAST
- NLOW_DIM=2
- OUTPUT_FILE=rmsd-embed
-... CLASSICAL_MDS
+data: COLLECT_FRAMES ATOMS=1-256
+mat: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=data
+mds: CLASSICAL_MDS USE_OUTPUT_DATA_FROM=mat NLOW_DIM=2
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=mds FILE=rmsd-embed
\endplumedfile
The following section is for people who are interested in how this method works in detail. A solid understanding of this material is
diff --git a/src/dimred/PCA.cpp b/src/dimred/PCA.cpp
index f8640e61b236e065e42027b96556280f0d4485c5..c343f0ef668f291fe19950e22915f9e5524ada51 100644
--- a/src/dimred/PCA.cpp
+++ b/src/dimred/PCA.cpp
@@ -63,14 +63,16 @@ The first two principal components will be output to a file called PCA-comp.pdb.
will be performed at the end of the simulation.
\plumedfile
-PCA METRIC=OPTIMAL ATOMS=1-22 STRIDE=1 NLOW_DIM=2 OFILE=PCA-comp.pdb
+ff: COLLECT_FRAMES ATOMS=1-22 STRIDE=1
+pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=OPTIMAL NLOW_DIM=2
+OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca FILE=PCA-comp.pdb
\endplumedfile
The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from changes in the six distances
seen in the previous lines. Notice that here the TYPE=EUCLIDEAN keyword is used to indicate that no alignment has to be done when calculating the various
elements of the covariance matrix from the input vectors. In this calculation the first two principal components will be output to a file called PCA-comp.pdb.
Trajectory frames will be collected every five steps and the PCA calculation is performed every 1000 steps. Consequently, if you run a 2000 step simulation the
-PCA analysis will be performed twice. The REWEIGHT_BIAS keyword in this input tells PLUMED that rather that ascribing a weight of one to each of the frames
+PCA analysis will be performed twice. The REWEIGHT_BIAS action in this input tells PLUMED that rather that ascribing a weight of one to each of the frames
when calculating averages and covariance matrices 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).
@@ -81,8 +83,12 @@ d3: DISTANCE ATOMS=1,4
d4: DISTANCE ATOMS=2,3
d5: DISTANCE ATOMS=2,4
d6: DISTANCE ATOMS=3,4
+rr: RESTRAINT ARG=d1 AT=0.1 KAPPA=10
+rbias: REWEIGHT_BIAS TEMP=300
-PCA ARG=d1,d2,d3,d4,d5,d6 METRIC=EUCLIDEAN STRIDE=5 RUN=1000 NLOW_DIM=2 REWEIGHT_BIAS OFILE=PCA-comp.pdb
+ff: COLLECT_FRAMES ARG=d1,d2,d3,d4,d5,d6 LOGWEIGHTS=rbias STRIDE=5
+pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=EUCLIDEAN NLOW_DIM=2
+OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca STRIDE=100 FILE=PCA-comp.pdb
\endplumedfile
*/
diff --git a/src/function/Custom.cpp b/src/function/Custom.cpp
index 03fc9936caec2a4c722b000744a34a07608be6f5..630cde788b2ef4dd5658e5fd0e3a5d2da24390d8 100644
--- a/src/function/Custom.cpp
+++ b/src/function/Custom.cpp
@@ -56,7 +56,7 @@ dAC: DISTANCE ATOMS=10,15
diff: CUSTOM 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
+METAD ARG=diff SIGMA=0.1 HEIGHT=0.5 BIASFACTOR=10 PACE=100
\endplumedfile
(see also \ref DISTANCE, \ref COMBINE, and \ref METAD).
Notice that forces applied to diff will be correctly propagated
@@ -77,7 +77,7 @@ CUSTOM ...
LABEL=theta
ARG=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z
VAR=ax,ay,az,bx,by,bz
- FUNC=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz))
+ FUNC=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz)))
PERIODIC=NO
... CUSTOM
PRINT ARG=theta
@@ -95,7 +95,7 @@ distance is larger than 0.5. You can do it with
d: DISTANCE ATOMS=10,15
m: CUSTOM 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
+PRINT ARG=d,m FILE=checkme
RESTRAINT ARG=d AT=0.5 KAPPA=10.0
\endplumedfile
(see also \ref DISTANCE, \ref PRINT, and \ref RESTRAINT)
@@ -197,7 +197,7 @@ Just replace \ref CUSTOM with \ref MATHEVAL.
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
+PRINT ARG=d,m FILE=checkme
RESTRAINT ARG=d AT=0.5 KAPPA=10.0
\endplumedfile
(see also \ref DISTANCE, \ref PRINT, and \ref RESTRAINT)
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index 5935ee07965453597d9c58ed03b97b5943512fce..91a0e811fc805e62d2e5e16d75b48deda0ee7463 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -57,7 +57,41 @@ 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
\endplumedfile
-In this second example is shown how to define a PATH in the \ref CONTACTMAP space:
+For this input you would then define the position of the reference coordinates in three separate pdb files. The contents of the
+file frame_1.pdb are shown below:
+
+\auxfile{frame_1.pdb}
+ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
+ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
+ATOM 6 OL ALA 1 -1.177 -0.889 2.401 1.00 1.00
+ATOM 7 NL ALA 1 -1.313 0.341 0.529 1.00 1.00
+ATOM 8 HL ALA 1 -1.845 0.961 -0.011 1.00 1.00
+END
+\endauxfile
+
+This is then frame.21.pdb:
+
+\auxfile{frame_21.pdb}
+ATOM 1 CL ALA 1 -3.089 1.850 1.546 1.00 1.00
+ATOM 5 CLP ALA 1 -1.667 1.457 1.629 1.00 1.00
+ATOM 6 OL ALA 1 -0.974 1.868 2.533 1.00 1.00
+ATOM 7 NL ALA 1 -1.204 0.683 0.642 1.00 1.00
+ATOM 8 HL ALA 1 -1.844 0.360 -0.021 1.00 1.00
+END
+\endauxfile
+
+and finally this is frame_42.pdb:
+
+\auxfile{frame_42.pdb}
+ATOM 1 CL ALA 1 -3.257 1.605 1.105 1.00 1.00
+ATOM 5 CLP ALA 1 -1.941 1.459 0.447 1.00 1.00
+ATOM 6 OL ALA 1 -1.481 2.369 -0.223 1.00 1.00
+ATOM 7 NL ALA 1 -1.303 0.291 0.647 1.00 1.00
+ATOM 8 HL ALA 1 -1.743 -0.379 1.229 1.00 1.00
+END
+\endauxfile
+
+This second example shows how to define a PATH in \ref CONTACTMAP space:
\plumedfile
CONTACTMAP ...
@@ -94,7 +128,7 @@ 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
\endplumedfile
-In this third example is shown how to define a PATH in the \ref PIV space:
+This third example shows how to define a PATH in \ref PIV space:
\plumedfile
PIV ...
diff --git a/src/function/Target.cpp b/src/function/Target.cpp
index 637330459676bcc155cdc8e0377c4ac9adb32322..ee87a44a23e340241d9264ef3912985a65f15524 100644
--- a/src/function/Target.cpp
+++ b/src/function/Target.cpp
@@ -86,13 +86,13 @@ The contents of the file containing the reference structure (reference.pdb) is s
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
quantities take in the reference configuration.
-\verbatim
+\auxfile{reference.pdb}
DESCRIPTION: a reference point.
REMARK WEIGHT=1.0
REMARK ARG=d1,d2
REMARK d1=1.0 d2=1.0
END
-\endverbatim
+\endauxfile
*/
//+ENDPLUMEDOC
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index 153f76f601daf6999cfb6ccb76ec57e41e99141c..a2ec2e6ad6612153d3e771233051d0c5d8d2dad7 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -44,8 +44,8 @@ can be done by outputting the derivatives calculated analytically and numericall
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.
\plumedfile
-DISTANCE ATOM=1,2 LABEL=distance
-DISTANCE ATOM=1,2 LABEL=distanceN NUMERICAL_DERIVATIVES
+DISTANCE ATOMS=1,2 LABEL=distance
+DISTANCE ATOMS=1,2 LABEL=distanceN NUMERICAL_DERIVATIVES
DUMPDERIVATIVES ARG=distance,distanceN STRIDE=1 FILE=deriv
\endplumedfile
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index 33ec80b8033e0ee969e1f541c1a179ec201fe910..00b490b1eebcc7c3c84ff03684dc819135b8ffb7 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -45,7 +45,7 @@ by specifying more than one argument. You can control the buffering of output us
The following input instructs plumed to write a file called forces that contains
the force acting on the distance between atoms 1 and 2.
\plumedfile
-DISTANCE ATOM=1,2 LABEL=distance
+DISTANCE ATOMS=1,2 LABEL=distance
DUMPFORCES ARG=distance STRIDE=1 FILE=forces
\endplumedfile
diff --git a/src/generic/DumpMassCharge.cpp b/src/generic/DumpMassCharge.cpp
index a3721dfb1cf832e472d3fbff4a2af9cd8b441527..0f60f682c2701f8c9b9c98a486637459f7bd6777 100644
--- a/src/generic/DumpMassCharge.cpp
+++ b/src/generic/DumpMassCharge.cpp
@@ -52,7 +52,7 @@ file that you use during an MD simulations:
\plumedfile
c1: COM ATOMS=1-10
c2: COM ATOMS=11-20
-PRINT ARG=c1,c2 FILE=colvar STRIDE=100
+DUMPATOMS ATOMS=c1,c2 FILE=coms.xyz STRIDE=100
DUMPMASSCHARGE FILE=mcfile
\endplumedfile
diff --git a/src/generic/FitToTemplate.cpp b/src/generic/FitToTemplate.cpp
index fbb275c941ec295b1ee73d090f60fa27f442be18..215918b66091bd687e3b6b3cf57ad1603e7422cc 100644
--- a/src/generic/FitToTemplate.cpp
+++ b/src/generic/FitToTemplate.cpp
@@ -120,15 +120,28 @@ FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=OPTIMAL
DUMPATOMS FILE=dump-after.xyz ATOMS=1-20
\endplumedfile
+In both these cases the reference structure should be provided in a reference pdb file such as the one below:
+
+\auxfile{ref.pdb}
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+END
+\endauxfile
+
In the following example you see two completely equivalent way
to restrain an atom close to a position that is defined in the reference
-frame of an aligned molecule. It could be for instance the center of mass
-of a ligand with respect to a protein
+frame of an aligned molecule. You could for instance use this command to calculate the
+position of the center of mass of a ligand after having aligned the atoms to the reference
+frame of the protein that is determined by aligning the atoms in the protein to the coordinates
+provided in the file ref.pdb
\plumedfile
# center of the ligand:
center: CENTER ATOMS=100-110
-FIT_TO_TEMPLATE REFERENCE=protein.pdb TYPE=OPTIMAL
+FIT_TO_TEMPLATE REFERENCE=ref.pdb TYPE=OPTIMAL
# place a fixed atom in the protein reference coordinates:
fix: FIXEDATOM AT=1.0,1.1,1.0
@@ -140,7 +153,7 @@ d: DISTANCE ATOMS=center,fix
RESTRAINT ARG=d AT=0.0 KAPPA=100.0
\endplumedfile
-Notice that you could have obtained an (almost) identical result adding a fictitious
+Notice that you could have obtained an (almost) identical result by adding a fictitious
atom to `ref.pdb` with the serial number corresponding to the atom labelled `center` (there is no automatic way
to get it, but in this example it should be the number of atoms of the system plus one),
and properly setting the weights for alignment and displacement in \ref RMSD.
diff --git a/src/generic/Group.cpp b/src/generic/Group.cpp
index 936f6709dc979b12fff699cbdcf312d63716bc18..59b26c780d33341308f4bfde9bf0fdfaa7c32a00 100644
--- a/src/generic/Group.cpp
+++ b/src/generic/Group.cpp
@@ -79,10 +79,11 @@ PRINT ARG=c FILE=colvar
Groups can be conveniently stored in a separate file.
E.g. one could create a file named `groups.dat` which reads
-\plumedfile
+\plumedincludefile
+# this is groups.dat
o: GROUP ATOMS=1,4,7,11,14
h: GROUP ATOMS=2,3,5,6,8,9,12,13
-\endplumedfile
+\endplumedincludefile
and then include it in the main 'plumed.dat' file
\plumedfile
INCLUDE FILE=groups.dat
@@ -93,10 +94,21 @@ PRINT ARG=c FILE=colvar
\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
+A GROMACS index file such as the one shown below:
+
+\auxfile{index.ndx}
+[ Protein ]
+1 3 5 7 9
+2 4 6 8 10
+[ Group2 ]
+30 31 32 33 34 35 36 37 38 39 40
+5
+\endauxfile
+
+can also be imported by using the GROUP keyword as shown below
\plumedfile
-# import group named 'protein' from file index.ndx
-pro: GROUP NDX_FILE=index.ndx NDX_GROUP=protein
+# 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
\endplumedfile
diff --git a/src/generic/Include.cpp b/src/generic/Include.cpp
index 3a3eb1eba80950372cd4edd49f92c28ed1498ec6..84bec5cb2cce4e19af97114527d187bfbaa22e22 100644
--- a/src/generic/Include.cpp
+++ b/src/generic/Include.cpp
@@ -54,10 +54,11 @@ d: DISTANCE ATOMS=c1,c2
PRINT ARG=d
\endplumedfile
where the content of file pippo.dat is
-\plumedfile
+\plumedincludefile
+# this is pippo.dat
c1: COM ATOMS=1-100
c2: COM ATOMS=101-202
-\endplumedfile
+\endplumedincludefile
The files in this example are rather short, but imagine a case like this one:
\plumedfile
@@ -66,7 +67,8 @@ c: COORDINATION GROUPA=groupa GROUPB=groupb R_0=0.5
METAD ARG=c HEIGHT=0.2 PACE=100 SIGMA=0.2 BIASFACTOR=5
\endplumedfile
Here `groups.dat` could be huge file containing group definitions such as
-\plumedfile
+\plumedincludefile
+# this is groups.dat
groupa: GROUP ...
ATOMS={
10
@@ -89,17 +91,17 @@ groupb: GROUP ...
121
}
...
-\endplumedfile
+\endplumedincludefile
So, included files are the best place where one can store long definitions.
Another case where INCLUDE is very useful is when running multi-replica simulations.
Here different replicas might have different input files, but perhaps a large part of the
input is shared. This part can be put in a common included file. For instance you could have
`common.dat`:
-\plumedfile
+\plumedincludefile
# this is common.dat
t: TORSION ATOMS=1,2,3,4
-\endplumedfile
+\endplumedincludefile
Then `plumed.0.dat`:
\plumedfile
# this is plumed.0.dat
@@ -120,21 +122,21 @@ This is true also for files opened by INCLUDE!
As an example, the same result of the inputs above could have been obtained using
`plumed.dat`:
-\plumedfile
+\plumedmultireplicafile{2}
# this is plumed.dat
t: TORSION ATOMS=1,2,3,4
-INCLUDE FILE=other.dat
-\endplumedfile
-Then `other.0.dat`:
-\plumedfile
-# this is other.0.dat
+INCLUDE FILE=other.inc
+\endplumedmultireplicafile
+Then `other.0.inc`:
+\plumedincludefile
+# this is other.0.inc
RESTRAINT ARG=t AT=1.0 KAPPA=10
-\endplumedfile
-And `other.1.dat`:
-\plumedfile
-# this is other.1.dat
+\endplumedincludefile
+And `other.1.inc`:
+\plumedincludefile
+# this is other.1.inc
RESTRAINT ARG=t AT=1.2 KAPPA=10
-\endplumedfile
+\endplumedincludefile
diff --git a/src/generic/Read.cpp b/src/generic/Read.cpp
index 3166e24e0f86cdb512ad3681a565044f3818b45d..55907468844635c2c73bda4046ff6ae96da16213 100644
--- a/src/generic/Read.cpp
+++ b/src/generic/Read.cpp
@@ -59,6 +59,19 @@ rphi2: READ FILE=input_colvar.data VALUES=phi2
PRINT ARG=rphi1,rphi2 STRIDE=500 FILE=output_colvar.data
\endplumedfile
+The file input_colvar.data is just a normal colvar file as shown below
+
+\auxfile{input_colvar.data}
+#! FIELDS time phi psi metad.bias metad.rbias metad.rct
+#! SET min_phi -pi
+#! SET max_phi pi
+#! SET min_psi -pi
+#! SET max_psi pi
+ 0.000000 -1.2379 0.8942 0.0000 0.0000 0.0000
+ 1.000000 -1.4839 1.0482 0.0000 0.0000 0.0089
+ 2.000000 -1.3243 0.6055 0.0753 0.0664 0.0184
+\endauxfile
+
*/
//+ENDPLUMEDOC
diff --git a/src/generic/ResetCell.cpp b/src/generic/ResetCell.cpp
index 9478e8601b404f4ead03bbca222b41d95b25024b..b08d9c223b4d145fda8fea2ba4964a714920e5f7 100644
--- a/src/generic/ResetCell.cpp
+++ b/src/generic/ResetCell.cpp
@@ -79,6 +79,16 @@ RESET_CELL TYPE=TRIANGULAR
DUMPATOMS FILE=dump-reset.xyz ATOMS=1-20
\endplumedfile
+The reference file for the FIT_TO_TEMPLATE is just a normal pdb file with the format shown below:
+
+\auxfile{ref.pdb}
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+END
+\endauxfile
*/
//+ENDPLUMEDOC
diff --git a/src/gridtools/DumpGrid.cpp b/src/gridtools/DumpGrid.cpp
index 1de9a9b6369b82605c885c6a6bd87a6de2948b73..26cd47a74dfd2d96154077f552f44462963a3709 100644
--- a/src/gridtools/DumpGrid.cpp
+++ b/src/gridtools/DumpGrid.cpp
@@ -130,7 +130,6 @@ HISTOGRAM ...
GRID_MAX=3.14,3.14
GRID_BIN=200,200
BANDWIDTH=0.05,0.05
- GRID_WFILE=histo
LABEL=hh
... HISTOGRAM
diff --git a/src/gridtools/FindContour.cpp b/src/gridtools/FindContour.cpp
index 97e68adb87a25ec383c06d8e25b62aff010bee78..4831ca8920ec7cc98798980d42a9ce64544055c2 100644
--- a/src/gridtools/FindContour.cpp
+++ b/src/gridtools/FindContour.cpp
@@ -74,16 +74,15 @@ FCCUBIC ...
ALPHA=27 PHI=0.0 THETA=-1.5708 PSI=-2.35619 LABEL=fcc
... FCCUBIC
-tfcc: MTRANSFORM_MORE DATA=fcc SWITCH={SMAP R_0=0.5 A=8 B=8}
+tfcc: MTRANSFORM_MORE DATA=fcc LOWMEM SWITCH={SMAP R_0=0.5 A=8 B=8}
center: CENTER_OF_MULTICOLVAR DATA=tfcc
-MULTICOLVARDENS ...
- DATA=tfcc ORIGIN=center DIR=xyz LABEL=dens
- NBINS=80,80,80 BANDWIDTH=1.0,1.0,1.0 STRIDE=25
- LABEL=dens STRIDE=1 CLEAR=1
-... MULTICOLVARDENS
+dens: MULTICOLVARDENS ...
+ DATA=tfcc ORIGIN=center DIR=xyz
+ NBINS=80,80,80 BANDWIDTH=1.0,1.0,1.0 STRIDE=1 CLEAR=1
+...
-FIND_CONTOUR GRID=dens CONTOUR=0.5 FILE=mycontour.dat
+FIND_CONTOUR GRID=dens CONTOUR=0.5 FILE=mycontour.xyz
\endplumedfile
*/
diff --git a/src/gridtools/FindSphericalContour.cpp b/src/gridtools/FindSphericalContour.cpp
index 018c11dc2e57a17f9b63ad128611ba4869fd91cd..ea59b860a4ff39b41d108837895b0db7cd05041c 100644
--- a/src/gridtools/FindSphericalContour.cpp
+++ b/src/gridtools/FindSphericalContour.cpp
@@ -89,7 +89,7 @@ cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
# Build a contact matrix
mat: CONTACT_MATRIX ATOMS=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
# Find largest cluster
-dfs: DFSCLUSTERING MATRIX=mat
+dfs: DFSCLUSTERING MATRIX=mat LOWMEM
clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1
# Find center of largest cluster
trans1: MTRANSFORM_MORE DATA=clust1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
@@ -97,7 +97,9 @@ cent: CENTER_OF_MULTICOLVAR DATA=trans1
# Calculate the phase field of the coordination
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
+sc: FIND_SPHERICAL_CONTOUR GRID=dens CONTOUR=0.85 INNER_RADIUS=10.0 OUTER_RADIUS=40.0 NPOINTS=100
+# And print the grid to a file
+GRID_TO_XYZ GRID=sc FILE=mysurface.xyz UNITS=A
\endplumedfile
*/
diff --git a/src/mapping/AdaptivePath.cpp b/src/mapping/AdaptivePath.cpp
index f140c414f52b82f8e9d5e780bcc542e183ddb9ff..85be6cca6b7b93af2a552873e0af12c2521c9c2d 100644
--- a/src/mapping/AdaptivePath.cpp
+++ b/src/mapping/AdaptivePath.cpp
@@ -59,19 +59,28 @@ MD based on the data accumulated during the preceding 50 time steps.
\plumedfile
d1: DISTANCE ATOMS=1,2 COMPONENTS
-pp: ADAPTIVE_PATH TYPE=EUCLIDEAN FIXED=5,15 UPDATE=50 WFILE=out-path.pdb WSTRIDE=50 REFERENCE=mypath.pdb
+pp: ADAPTIVE_PATH TYPE=EUCLIDEAN FIXED=2,5 UPDATE=50 WFILE=out-path.pdb WSTRIDE=50 REFERENCE=mypath.pdb
PRINT ARG=d1.x,d1.y,pp.* FILE=colvar
\endplumedfile
In the case above the distance between frames is calculated based on the \f$x\f$ and \f$y\f$ components of the vector connecting
atoms 1 and 2. As such an extract from the input reference path (mypath.pdb) would look as follows:
-\verbatim
+\auxfile{mypath.pdb}
REMARK ARG=d1.x,d1.y d1.x=1.12 d1.y=-.60
END
REMARK ARG=d1.x,d1.y d1.x=.99 d1.y=-.45
END
-\endverbatim
+REMARK ARG=d1.x,d1.y d1.x=.86 d1.y=-.30
+END
+REMARK ARG=d1.x,d1.y d1.x=.73 d1.y=-.15
+END
+REMARK ARG=d1.x,d1.y d1.x=.60 d1.y=0
+END
+REMARK ARG=d1.x,d1.y d1.x=.47 d1.y=.15
+END
+
+\endauxfile
Notice that one can also use RMSD frames in place of arguments like those above.
diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index 224dfb7493b34491f291e9398d00454eefe482dc..3f296100ea9b53100a0d2d29431f1afc93ab1b51 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -86,7 +86,8 @@ the matrix \f$A\f$ above. These directions can be specified by specifying a sec
be constructed by calculating the displacement of this second configuration from the reference configuration. A pdb input prepared
in this way would look as follows:
-\verbatim
+\auxfile{reference.pdb}
+REMARK TYPE=OPTIMAL
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
@@ -95,6 +96,7 @@ ATOM 15 C ALA 2 19.422 7.978 -14.536 1.00 1.00
ATOM 20 HH31 NME 3 20.122 -9.928 -17.746 1.00 1.00
ATOM 21 HH32 NME 3 18.572 -13.148 -16.346 1.00 1.00
END
+REMARK TYPE=OPTIMAL
ATOM 2 CH3 ACE 1 13.932 -14.718 -6.016 1.00 1.00
ATOM 5 C ACE 1 20.312 -9.928 -5.946 1.00 1.00
ATOM 9 CA ALA 2 18.462 -11.088 -8.986 1.00 1.00
@@ -103,7 +105,7 @@ ATOM 15 C ALA 2 19.422 7.978 -12.536 1.00 1.00
ATOM 20 HH31 NME 3 20.122 -9.928 -17.746 1.00 1.00
ATOM 21 HH32 NME 3 18.572 -13.148 -16.346 1.00 1.00
END
-\endverbatim
+\endauxfile
Alternatively, the second configuration can specify the components of \f$A\f$ explicitly. In this case you need to include the
keyword TYPE=DIRECTION in the remarks to the pdb as shown below.
diff --git a/src/mapping/Path.cpp b/src/mapping/Path.cpp
index 1a4c3cb9f78cfbf9e203bc7d5b9c998f47960440..56288018cbc8bff4042ef2f0cd438bba6171dcc5 100644
--- a/src/mapping/Path.cpp
+++ b/src/mapping/Path.cpp
@@ -70,14 +70,33 @@ The values of \f$s\f$ and \f$z\f$ can then be referenced using the gspath and gz
\par Examples
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.
\plumedfile
p1: PATH REFERENCE=file.pdb TYPE=OPTIMAL LAMBDA=500.0
-PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f
+PRINT ARG=p1.spath,p1.zpath STRIDE=1 FILE=colvar FMT=%8.4f
\endplumedfile
+The reference frames in the path are defined in the pdb file shown below. In this frame
+each configuration in the path is separated by a line containing just the word END.
+
+\auxfile{file.pdb}
+ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
+ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
+ATOM 6 OL ALA 1 -1.177 -0.889 2.401 1.00 1.00
+ATOM 7 NL ALA 1 -1.313 0.341 0.529 1.00 1.00
+END
+ATOM 1 CL ALA 1 -3.175 0.365 2.024 1.00 1.00
+ATOM 5 CLP ALA 1 -1.814 -0.106 1.685 1.00 1.00
+ATOM 6 OL ALA 1 -1.201 -0.849 2.425 1.00 1.00
+ATOM 7 NL ALA 1 -1.296 0.337 0.534 1.00 1.00
+END
+ATOM 1 CL ALA 1 -2.990 0.383 2.277 1.00 1.00
+ATOM 5 CLP ALA 1 -1.664 -0.085 1.831 1.00 1.00
+ATOM 6 OL ALA 1 -0.987 -0.835 2.533 1.00 1.00
+ATOM 7 NL ALA 1 -1.227 0.364 0.646 1.00 1.00
+END
+\endauxfile
+
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 algebraic expressions that are used by default.
@@ -93,53 +112,18 @@ Notice that the LAMBDA parameter is not required here as we are not calculating
using the algebraic formulae defined earlier. The positions of the frames in the path are defined
in the file epath.pdb. An extract from this file looks as shown below.
-\verbatim
+\auxfile{epath.pdb}
REMARK ARG=t1,t2 t1=-4.25053 t2=3.88053
END
REMARK ARG=t1,t2 t1=-4.11 t2=3.75
END
REMARK ARG=t1,t2 t1=-3.96947 t2=3.61947
END
-\endverbatim
+\endauxfile
The remarks in this pdb file tell PLUMED the labels that are being used to define the position in the
high dimensional space and the values that these arguments have at each point on the path.
-The following input instructs PLUMED to calculate the values of the path collective variables. The frames that make up this
-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.
-
-\plumedfile
-p2: PATH REFERENCE=all.pdb LAMBDA=69087
-PRINT ARG=p2.spath,p2.zpath STRIDE=1 FILE=colvar
-\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:
-
-\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
-\endplumedfile
-
-The corresponding pdb file containing the definitions of the frames in the path would then look like this:
-
-\verbatim
-DESCRIPTION: a defintiion of a PATH
-REMARK TYPE=EUCLIDEAN
-REMARK ARG=d1,d2
-REMARK d1=1.0 d2=1.0
-END
-REMARK TYPE=EUCLIDEAN
-REMARK ARG=d1,d2
-REMARK d1=2.0 d2=2.0
-END
-\endverbatim
-
-For each frame in the path you must specify the arguments that should be used to calculate the distance between the instantaneous configuration
-of the system and the reference configurations together with the values that these arguments take in each of the reference configurations.
-
*/
//+ENDPLUMEDOC
diff --git a/src/mapping/PropertyMap.cpp b/src/mapping/PropertyMap.cpp
index ac13aad4a192c1ba0499df5504c0135bef8d48b3..0b8e2b87a00838692f5d324b2b100b1dfba9530d 100644
--- a/src/mapping/PropertyMap.cpp
+++ b/src/mapping/PropertyMap.cpp
@@ -55,7 +55,7 @@ PRINT ARG=p2.X,p2.Y,p2.zpath STRIDE=1 FILE=colvar
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.
-\verbatim
+\auxfile{allv.pdb}
REMARK X=1 Y=2
ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
@@ -87,7 +87,7 @@ ATOM 17 NR ALA 1 1.380 0.537 1.968 1.00 1.00
ATOM 18 HR ALA 1 0.764 -0.060 2.461 1.00 1.00
ATOM 19 CR ALA 1 2.431 1.195 2.683 1.00 1.00
END
-\endverbatim
+\endauxfile
*/
//+ENDPLUMEDOC
diff --git a/src/multicolvar/Bridge.cpp b/src/multicolvar/Bridge.cpp
index e78584427b01317b8f993eeb41240533a8d6af88..997ccc0219cc79ba765c7bf8205814a58ffec467 100644
--- a/src/multicolvar/Bridge.cpp
+++ b/src/multicolvar/Bridge.cpp
@@ -52,8 +52,8 @@ that are bridging between atoms 1-10 and atoms 11-20 and to print the value
to a file
\plumedfile
-BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 LABEL=w1
-PRINT ARG=a1.mean FILE=colvar
+w1: BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 SWITCH={RATIONAL R_0=0.2}
+PRINT ARG=w1 FILE=colvar
\endplumedfile
*/
diff --git a/src/multicolvar/CenterOfMultiColvar.cpp b/src/multicolvar/CenterOfMultiColvar.cpp
index 5917e8006fb263851456c02f2c83512e86705f99..fe28d03f52c99e714cc2eea8d6f4f85d5bc2a179 100644
--- a/src/multicolvar/CenterOfMultiColvar.cpp
+++ b/src/multicolvar/CenterOfMultiColvar.cpp
@@ -56,7 +56,7 @@ numbers should have a high weight in the weighted average you are using to calcu
You can thus calculate the position of the droplet using an input like the one shown below:
\plumedfile
-c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
+c1: COORDINATIONNUMBER LOWMEM SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
cc: CENTER_OF_MULTICOLVAR DATA=c1
\endplumedfile
diff --git a/src/multicolvar/Density.cpp b/src/multicolvar/Density.cpp
index f45deadec6599b31058469df8461e9c9ab914a5a..e8b9755df3acf0c04ff3c31521e14a9ba6837f2d 100644
--- a/src/multicolvar/Density.cpp
+++ b/src/multicolvar/Density.cpp
@@ -42,7 +42,7 @@ The following example calculates the number of atoms in one half of the simulati
\plumedfile
DENSITY SPECIES=1-100 LABEL=d
-AROUND ARG=d XLOWER=0.0 XUPPER=0.5 LABEL=d1
+AROUND ATOM=101 DATA=d SIGMA=0.1 XLOWER=0.0 XUPPER=0.5 LABEL=d1
PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f
\endplumedfile
diff --git a/src/multicolvar/DihedralCorrelation.cpp b/src/multicolvar/DihedralCorrelation.cpp
index 65dd6358aaabb757b68bcfed18701c70aed06c56..4460d24913073cdd9e97a0d4c426e2a82195caac 100644
--- a/src/multicolvar/DihedralCorrelation.cpp
+++ b/src/multicolvar/DihedralCorrelation.cpp
@@ -67,11 +67,11 @@ about the topology of the protein molecule. This means that you can specify tor
\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
-DIHCOR ...
+dih: DIHCOR ...
ATOMS1=@phi-3,@psi-3
ATOMS2=@psi-3,@phi-4
-ATOMS4=@phi-4,@psi-4
-... DIHCOR
+ATOMS3=@phi-4,@psi-4
+...
PRINT ARG=dih FILE=colvar STRIDE=10
\endplumedfile
diff --git a/src/multicolvar/Distances.cpp b/src/multicolvar/Distances.cpp
index 6a931c118b0fe8f5fd362fed16f99454115d92ca..5fc6026921b0360ed77543ad802e60ee30596d15 100644
--- a/src/multicolvar/Distances.cpp
+++ b/src/multicolvar/Distances.cpp
@@ -43,7 +43,7 @@ Calculate the distances between one or many pairs of atoms. You can then calcul
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.
\plumedfile
-DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
+d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
PRINT ARG=d1.min
\endplumedfile
(See also \ref PRINT).
@@ -52,15 +52,15 @@ The following input tells plumed to calculate the distances between atoms 3 and
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.
\plumedfile
-DISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.lt0.1
+d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.lessthan
\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.
\plumedfile
-DISTANCES GROUP=1-3 MEAN LABEL=d1
+d1: DISTANCES GROUP=1-3 MEAN
PRINT ARG=d1.mean
\endplumedfile
(See also \ref PRINT)
@@ -69,8 +69,8 @@ The following input tells plumed to calculate all the distances between the atom
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.
\plumedfile
-DISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.gt0.1
+d1: DISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.morethan
\endplumedfile
(See also \ref PRINT \ref switchingfunction)
@@ -103,13 +103,13 @@ can calculate the number of distances less than 1.0, the minimum distance, the n
2.0 and the number of distances between 1.0 and 2.0 by using the following command:
\plumedfile
-DISTANCES ...
+d1: DISTANCES ...
GROUPA=1-10 GROUPB=11-20
LESS_THAN={RATIONAL R_0=1.0}
MORE_THAN={RATIONAL R_0=2.0}
BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0}
MIN={BETA=500.}
-... DISTANCES
+...
PRINT ARG=d1.lessthan,d1.morethan,d1.between,d1.min FILE=colvar STRIDE=10
\endplumedfile
(see \ref DISTANCES and \ref PRINT)
diff --git a/src/multicolvar/FilterMoreThan.cpp b/src/multicolvar/FilterMoreThan.cpp
index 958ff5168dc45110ca2e2733bcc46989a55823b9..cf324540a7574f4d3b628f0929b67e09f1f13e3b 100644
--- a/src/multicolvar/FilterMoreThan.cpp
+++ b/src/multicolvar/FilterMoreThan.cpp
@@ -116,7 +116,7 @@ to a second coordination number calculation. This second coordination number th
two-coordinated atoms that each of the two-coordinated atoms is bound to.
\plumedfile
-1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}
+c1: 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}
\endplumedfile
diff --git a/src/multicolvar/InPlaneDistances.cpp b/src/multicolvar/InPlaneDistances.cpp
index 197c24b7875ba11da4cbd341ab51a539564fcccf..1d264bb4950886886eba709453d593aa442fad9a 100644
--- a/src/multicolvar/InPlaneDistances.cpp
+++ b/src/multicolvar/InPlaneDistances.cpp
@@ -92,11 +92,10 @@ InPlaneDistances::InPlaneDistances(const ActionOptions&ao):
readThreeGroups("GROUP","VECTORSTART","VECTOREND",false,false,all_atoms);
setupMultiColvarBase( all_atoms );
- // Check atoms are OK
- if( getFullNumberOfTasks()!=getNumberOfAtoms()-2 ) error("you should specify one atom for VECTORSTART and one atom for VECTOREND only");
-
// Setup the multicolvar base
setupMultiColvarBase( all_atoms ); readVesselKeywords();
+ // Check atoms are OK
+ if( getFullNumberOfTasks()!=getNumberOfAtoms()-2 ) error("you should specify one atom for VECTORSTART and one atom for VECTOREND only");
// And check everything has been read in correctly
checkRead();
diff --git a/src/multicolvar/LocalAverage.cpp b/src/multicolvar/LocalAverage.cpp
index db52c55ba7a30798380bd9900978ed4a4fe1c318..aceadee9d592270de14ecfef0c8a187dc3ff7cb4 100644
--- a/src/multicolvar/LocalAverage.cpp
+++ b/src/multicolvar/LocalAverage.cpp
@@ -61,7 +61,7 @@ spherical regions. The number of averaged coordination numbers that are greater
\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
+LOCAL_AVERAGE SPECIES=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MORE_THAN={RATIONAL R_0=4} LABEL=la
PRINT ARG=la.* FILE=colvar
\endplumedfile
@@ -71,7 +71,7 @@ quantities that were used in the paper by Lechner and Dellago \cite dellago-q6
\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
+LOCAL_AVERAGE SPECIES=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=la
PRINT ARG=la.* FILE=colvar
\endplumedfile
diff --git a/src/multicolvar/NumberOfLinks.cpp b/src/multicolvar/NumberOfLinks.cpp
index 833763164b3dfc5ee4ab53a65ee04b6a60048a2c..bd07cc7de507e05e0509902a8dfbe69a53b46340 100644
--- a/src/multicolvar/NumberOfLinks.cpp
+++ b/src/multicolvar/NumberOfLinks.cpp
@@ -45,7 +45,7 @@ this quantity to a file.
\plumedfile
DENSITY SPECIES=1-64 LABEL=d1
-NLINKS ARG=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
+NLINKS GROUP=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar
\endplumedfile
@@ -56,7 +56,7 @@ dot product of the Q6 vectors on adjacent atoms to measure whether or not two at
\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
+NLINKS GROUP=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd
PRINT ARG=dd FILE=colvar
\endplumedfile
diff --git a/src/multicolvar/Torsions.cpp b/src/multicolvar/Torsions.cpp
index 360344ddc66e94fc08292a441217c9bed5d9b84b..13889c1a1385a4b8709e5cb27c6f7cb99af1a9f7 100644
--- a/src/multicolvar/Torsions.cpp
+++ b/src/multicolvar/Torsions.cpp
@@ -45,6 +45,7 @@ TORSIONS ...
ATOMS1=168,170,172,188
ATOMS2=170,172,188,190
ATOMS3=188,190,192,230
+BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
LABEL=ab
... TORSIONS
PRINT ARG=ab.* FILE=colvar STRIDE=10
@@ -60,9 +61,10 @@ TORSIONS ...
ATOMS1=@phi-3
ATOMS2=@psi-3
ATOMS3=@phi-4
+BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
LABEL=ab
... TORSIONS
-PRINT ARG=ab FILE=colvar STRIDE=10
+PRINT ARG=ab.* FILE=colvar STRIDE=10
\endplumedfile
Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
diff --git a/src/multicolvar/VolumeAround.cpp b/src/multicolvar/VolumeAround.cpp
index bddef4b2e464c9e6500d2ff1d4eb4b5ed337d75d..fd3d7b2322a8970639aa9f2237d42fcc3119998b 100644
--- a/src/multicolvar/VolumeAround.cpp
+++ b/src/multicolvar/VolumeAround.cpp
@@ -57,7 +57,7 @@ that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The
\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
+AROUND DATA=c ATOM=c1 XLOWER=-2.0 XUPPER=2.0 SIGMA=0.1 MEAN LABEL=s
\endplumedfile
*/
diff --git a/src/multicolvar/VolumeBetweenContours.cpp b/src/multicolvar/VolumeBetweenContours.cpp
index edd3d3ef5c6290aa237909ec16d472a2892dc534..8679b9c7b67b4770219862a87ae876a4c5b95d4b 100644
--- a/src/multicolvar/VolumeBetweenContours.cpp
+++ b/src/multicolvar/VolumeBetweenContours.cpp
@@ -51,7 +51,7 @@ that are specified in the DENSITY action that are within a region where the dens
\plumedfile
d1: DENSITY SPECIES=14401-74134:3 LOWMEM
fi: INENVELOPE DATA=d1 ATOMS=1-14400 CONTOUR={RATIONAL D_0=2.0 R_0=1.0} BANDWIDTH=0.1,0.1,0.1 LOWMEM
-PRINT ARG=fi,rr.* FILE=colvar
+PRINT ARG=fi FILE=colvar
\endplumedfile
*/
diff --git a/src/multicolvar/VolumeCavity.cpp b/src/multicolvar/VolumeCavity.cpp
index 65aaed7eca7bd575e82c6a7d06145fc33baa3037..a09a6b01aafa62efbc7f0689c59429756849eeea 100644
--- a/src/multicolvar/VolumeCavity.cpp
+++ b/src/multicolvar/VolumeCavity.cpp
@@ -95,7 +95,7 @@ molecules in the protein channel described above. The average coordination numb
numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
\plumedfile
-d1: COORDINATIONNUMBER SPECIES=20-500
+d1: COORDINATIONNUMBER SPECIES=20-500 R_0=0.1
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
\endplumedfile
diff --git a/src/multicolvar/VolumeInCylinder.cpp b/src/multicolvar/VolumeInCylinder.cpp
index 3c18c238f0c2e38cfdd14abc1f2e37b753370213..c80e753e8838c59e484bfe38e77be2010229f8bc 100644
--- a/src/multicolvar/VolumeInCylinder.cpp
+++ b/src/multicolvar/VolumeInCylinder.cpp
@@ -60,7 +60,7 @@ of radius 1.5 nm that is centered on the position of atom 101 and that has its l
\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
+d2: INCYLINDER ATOM=101 DATA=c1 DIRECTION=Z RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 MEAN
PRINT ARG=d2.* FILE=colvar
\endplumedfile
diff --git a/src/multicolvar/VolumeInSphere.cpp b/src/multicolvar/VolumeInSphere.cpp
index 4f47e8ccd590c8d3158adc6c582d99da38ef1532..44606f81278636553874b718cb3001deaa7067ac 100644
--- a/src/multicolvar/VolumeInSphere.cpp
+++ b/src/multicolvar/VolumeInSphere.cpp
@@ -59,7 +59,7 @@ of radius 1.5 nm that is centered on the position of atom 101.
\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
+d2: INSPHERE ATOM=101 DATA=c1 RADIUS={TANH R_0=1.5} MEAN
PRINT ARG=d2.* FILE=colvar
\endplumedfile
diff --git a/src/multicolvar/VolumeTetrapore.cpp b/src/multicolvar/VolumeTetrapore.cpp
index 70793a58391a7af7c4ba4b3574cb3b50e74eb544..70b1f02f0507f3f7636305b76803171440a11f4d 100644
--- a/src/multicolvar/VolumeTetrapore.cpp
+++ b/src/multicolvar/VolumeTetrapore.cpp
@@ -103,7 +103,7 @@ molecules in the tetrahedral cavity described above. The average coordination n
numbers more than 4 is then calculated. The values of these two quantities are given the labels cav.mean and cav.morethan
\plumedfile
-d1: COORDINATIONNUMBER SPECIES=20-500
+d1: COORDINATIONNUMBER SPECIES=20-500 R_0=0.1
CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav
\endplumedfile
diff --git a/src/multicolvar/XDistances.cpp b/src/multicolvar/XDistances.cpp
index 73c22269e8c88a8477218b3efe801684c9d41ca5..90d99c879b20b74a35c66eaacf61ffa04d6073a1 100644
--- a/src/multicolvar/XDistances.cpp
+++ b/src/multicolvar/XDistances.cpp
@@ -42,7 +42,7 @@ The following input tells plumed to calculate the x-component of the vector conn
the x-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
\plumedfile
-XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
+d1: XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
PRINT ARG=d1.min
\endplumedfile
(See also \ref PRINT).
@@ -52,8 +52,8 @@ The following input tells plumed to calculate the x-component of the vector conn
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.
\plumedfile
-XDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.lt0.1
+d1: XDISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.lessthan
\endplumedfile
(See also \ref PRINT \ref switchingfunction).
@@ -61,8 +61,8 @@ The following input tells plumed to calculate the x-components of all the distin
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.
\plumedfile
-XDISTANCES GROUP=1-3 AVERAGE LABEL=d1
-PRINT ARG=d1.average
+d1: XDISTANCES GROUP=1-3 MEAN
+PRINT ARG=d1.mean
\endplumedfile
(See also \ref PRINT)
@@ -70,8 +70,8 @@ The following input tells plumed to calculate all the vectors connecting the the
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.
\plumedfile
-XDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.gt0.1
+d1: XDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.morethan
\endplumedfile
(See also \ref PRINT \ref switchingfunction)
*/
@@ -88,7 +88,7 @@ The following input tells plumed to calculate the y-component of the vector conn
the y-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
\plumedfile
-YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
+d1: YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
PRINT ARG=d1.min
\endplumedfile
(See also \ref PRINT).
@@ -98,8 +98,8 @@ The following input tells plumed to calculate the y-component of the vector conn
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.
\plumedfile
-YDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.lt0.1
+d1: YDISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.lessthan
\endplumedfile
(See also \ref PRINT \ref switchingfunction).
@@ -107,8 +107,8 @@ The following input tells plumed to calculate the y-components of all the distin
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.
\plumedfile
-YDISTANCES GROUP=1-3 AVERAGE LABEL=d1
-PRINT ARG=d1.average
+d1: YDISTANCES GROUP=1-3 MEAN
+PRINT ARG=d1.mean
\endplumedfile
(See also \ref PRINT)
@@ -116,8 +116,8 @@ The following input tells plumed to calculate all the vectors connecting the the
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.
\plumedfile
-YDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.gt0.1
+d1: YDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.morethan
\endplumedfile
(See also \ref PRINT \ref switchingfunction)
@@ -135,7 +135,7 @@ The following input tells plumed to calculate the z-component of the vector conn
the z-component of the vector connecting atom 1 to atom 2. The minimum of these two quantities is then
printed
\plumedfile
-ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
+d1: ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
PRINT ARG=d1.min
\endplumedfile
(See also \ref PRINT).
@@ -145,8 +145,8 @@ The following input tells plumed to calculate the z-component of the vector conn
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.
\plumedfile
-ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 LABEL=d1 LESS_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.lt0.1
+d1: ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.lessthan
\endplumedfile
(See also \ref PRINT \ref switchingfunction).
@@ -154,8 +154,8 @@ The following input tells plumed to calculate the z-components of all the distin
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.
\plumedfile
-ZDISTANCES GROUP=1-3 AVERAGE LABEL=d1
-PRINT ARG=d1.average
+d1: ZDISTANCES GROUP=1-3 MEAN
+PRINT ARG=d1.mean
\endplumedfile
(See also \ref PRINT)
@@ -163,8 +163,8 @@ The following input tells plumed to calculate all the vectors connecting the the
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.
\plumedfile
-ZDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
-PRINT ARG=d1.gt0.1
+d1: ZDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}
+PRINT ARG=d1.morethan
\endplumedfile
(See also \ref PRINT \ref switchingfunction)
diff --git a/src/multicolvar/XYDistances.cpp b/src/multicolvar/XYDistances.cpp
index f41f4c4db576d233e1d2a5e52a22202acd783619..e286aeccc7629f8e617c7b1738f78cfcdf48a87d 100644
--- a/src/multicolvar/XYDistances.cpp
+++ b/src/multicolvar/XYDistances.cpp
@@ -44,7 +44,7 @@ to atom 5 projected in the xy-plane and the projection of the length of the vect
the vector connecting atom 1 to atom 2 in the xy-plane. The minimum of these two quantities is then
printed
\plumedfile
-XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
+d1: XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
PRINT ARG=d1.min
\endplumedfile
(See also \ref PRINT).
@@ -66,7 +66,7 @@ to atom 5 projected in the xz-plane and the projection of the length of the vect
the vector connecting atom 1 to atom 2 in the xz-plane. The minimum of these two quantities is then
printed
\plumedfile
-XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
+d1: XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
PRINT ARG=d1.min
\endplumedfile
(See also \ref PRINT).
@@ -88,7 +88,7 @@ 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
\plumedfile
-YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
+d1: YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
PRINT ARG=d1.min
\endplumedfile
(See also \ref PRINT).
diff --git a/src/multicolvar/XYTorsion.cpp b/src/multicolvar/XYTorsion.cpp
index 714e75f62f24488223573ee55d17fa9d12c9758e..8788ddeb00db7f8331ff1c26ee9d26996a1737fb 100644
--- a/src/multicolvar/XYTorsion.cpp
+++ b/src/multicolvar/XYTorsion.cpp
@@ -42,8 +42,8 @@ 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
\plumedfile
-XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
-PRINT ARG=d1.min
+d1: XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
+PRINT ARG=d1.between
\endplumedfile
(See also \ref PRINT).
*/
@@ -58,8 +58,8 @@ 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
\plumedfile
-XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
-PRINT ARG=d1.min
+d1: XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
+PRINT ARG=d1.*
\endplumedfile
(See also \ref PRINT).
*/
@@ -74,8 +74,8 @@ 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
\plumedfile
-YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
-PRINT ARG=d1.min
+d1: YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
+PRINT ARG=d1.*
\endplumedfile
(See also \ref PRINT).
*/
@@ -90,8 +90,8 @@ 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
\plumedfile
-YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
-PRINT ARG=d1.min
+d1: YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
+PRINT ARG=d1.*
\endplumedfile
(See also \ref PRINT).
*/
@@ -106,8 +106,8 @@ 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
\plumedfile
-ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
-PRINT ARG=d1.min
+d1: ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
+PRINT ARG=d1.*
\endplumedfile
(See also \ref PRINT).
*/
@@ -122,8 +122,8 @@ 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
\plumedfile
-ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1
-PRINT ARG=d1.min
+d1: ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
+PRINT ARG=d1.*
\endplumedfile
(See also \ref PRINT).
*/
diff --git a/src/pamm/PAMM.cpp b/src/pamm/PAMM.cpp
index 40703b088821dca9a81d11e2305f3ff7939fb5c4..7e847bc5fbb0777fd2e07ca5263b919558f889b7 100644
--- a/src/pamm/PAMM.cpp
+++ b/src/pamm/PAMM.cpp
@@ -63,19 +63,20 @@ In this example I will explain in detail what the following input is computing:
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
-p: PAMM DATA=phi,psi CLUSTERS=clusters.dat MEAN1={COMPONENT=1} MEAN2={COMPONENT=2}
-PRINT ARG=p.mean-1,mean-2 FILE=colvar
+p: PAMM DATA=phi,psi CLUSTERS=clusters.pamm MEAN1={COMPONENT=1} MEAN2={COMPONENT=2}
+PRINT ARG=p.mean-1,p.mean-2 FILE=colvar
\endplumedfile
-The best place to start our explanation is to look at the contents of the clusters.dat file
+The best place to start our explanation is to look at the contents of the clusters.pamm file
-\verbatim
+\auxfile{clusters.pamm}
#! FIELDS height phi psi sigma_phi_phi sigma_phi_psi sigma_psi_phi sigma_psi_psi
#! SET multivariate von-misses
#! SET kerneltype gaussian
- 0.4 -1.0 -1.0 0.2 -0.1 -0.1 0.2
- 0.6 1.0 +1.0 0.1 -0.03 -0.03 0.1
-\endverbatim
+ 2.97197455E-0001 -1.91983118E+0000 2.25029540E+0000 2.45960237E-0001 -1.30615381E-0001 -1.30615381E-0001 2.40239117E-0001
+ 2.29131448E-0002 1.39809354E+0000 9.54585380E-0002 9.61755708E-0002 -3.55657919E-0002 -3.55657919E-0002 1.06147253E-0001
+ 5.06676398E-0001 -1.09648066E+0000 -7.17867907E-0001 1.40523052E-0001 -1.05385552E-0001 -1.05385552E-0001 1.63290557E-0001
+\endauxfile
This files contains the parameters of two two-dimensional Gaussian functions. Each of these Gaussian kernels has a weight, \f$w_k\f$,
a vector that specifies the position of its center, \f$\mathbf{c}_k\f$, and a covariance matrix, \f$\Sigma_k\f$. The \f$\phi_k\f$ functions that
diff --git a/src/vatom/FixedAtom.cpp b/src/vatom/FixedAtom.cpp
index 0d4707eb37fa4907deff00346e9198342de9acda..0b5ea2c2df1c7cff2622f87d13a6be2720216464 100644
--- a/src/vatom/FixedAtom.cpp
+++ b/src/vatom/FixedAtom.cpp
@@ -58,8 +58,8 @@ an: ANGLE ATOMS=a,b,15,20
RESTRAINT ARG=an AT=0.0 KAPPA=100.0
\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
+The following input instructs plumed to align a protein to a template
+and to then compute the distance between one of the atoms in the protein and the point
(10,20,30).
\plumedfile
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE
@@ -68,6 +68,17 @@ d: DISTANCE ATOMS=a,20
PRINT ARG=d FILE=colvar
\endplumedfile
+The reference structure to align to is provided in a pdb file called ref.pdb as shown below:
+
+\auxfile{ref.pdb}
+ATOM 8 HT3 ALA 2 -1.480 -1.560 1.212 1.00 1.00 DIA H
+ATOM 9 CAY ALA 2 -0.096 2.144 -0.669 1.00 1.00 DIA C
+ATOM 10 HY1 ALA 2 0.871 2.385 -0.588 1.00 1.00 DIA H
+ATOM 12 HY3 ALA 2 -0.520 2.679 -1.400 1.00 1.00 DIA H
+ATOM 14 OY ALA 2 -1.139 0.931 -0.973 1.00 1.00 DIA O
+END
+\endauxfile
+
*/
//+ENDPLUMEDOC
diff --git a/src/ves/Opt_BachAveragedSGD.cpp b/src/ves/Opt_BachAveragedSGD.cpp
index 57757f54595c761c16a39019aace765c901fc4f7..34151444fdbe3fafd9ed49bced4113e9ac530308 100644
--- a/src/ves/Opt_BachAveragedSGD.cpp
+++ b/src/ves/Opt_BachAveragedSGD.cpp
@@ -138,7 +138,7 @@ is updated every 500 iterations (e.g. every 1000 ps). The target distribution is
also output to a file every 2000 iterations (the TARGETDIST_OUTPUT keyword).
Here we also employ MULTIPLE_WALKERS flag to enable the usage of
multiple walkers.
-\plumedfile
+\plumedmultireplicafile{2}
phi: TORSION ATOMS=5,7,9,15
psi: TORSION ATOMS=7,9,15,17
@@ -172,7 +172,7 @@ OPT_AVERAGED_SGD ...
TARGETDIST_STRIDE=500
TARGETDIST_OUTPUT=2000
... OPT_AVERAGED_SGD
-\endplumedfile
+\endplumedmultireplicafile
diff --git a/src/ves/TD_Custom.cpp b/src/ves/TD_Custom.cpp
index 949e6d8f0dc0bc9331f6a1773fafc7f35cc2e9f8..0845d3b03696bd212b0902c67408dcbba34352cd 100644
--- a/src/ves/TD_Custom.cpp
+++ b/src/ves/TD_Custom.cpp
@@ -104,7 +104,7 @@ variable. It is also possible to use the \f$k_B T\f$ variable. The following
syntax will give the exact same results as the syntax above
\plumedfile
TD_CUSTOM ...
- FUNCTION=exp(-(1.0/(kBT*10.0))*FE)}
+ FUNCTION=exp(-(1.0/(kBT*10.0))*FE)
LABEL=td
... TD_CUSTOM
\endplumedfile
diff --git a/src/ves/TD_Grid.cpp b/src/ves/TD_Grid.cpp
index 97ba49457bb4623a1f304b8b2dc896f59673cb04..17d7cd7682469399298865e8b5cd8b2e1105ca54 100644
--- a/src/ves/TD_Grid.cpp
+++ b/src/ves/TD_Grid.cpp
@@ -78,6 +78,24 @@ file.
td: TD_GRID FILE=input-grid.data
\endplumedfile
+The input grid is then specified using the usual format employed by PLUMED an example of which
+is shown below:
+
+\auxfile{input-grid.data}
+#! FIELDS d1 external.bias der_d1
+#! SET min_d1 1.14
+#! SET max_d1 1.32
+#! SET nbins_d1 6
+#! SET periodic_d1 false
+ 1.1400 0.0031 0.1101
+ 1.1700 0.0086 0.2842
+ 1.2000 0.0222 0.6648
+ 1.2300 0.0521 1.4068
+ 1.2600 0.1120 2.6873
+ 1.2900 0.2199 4.6183
+ 1.3200 0.3948 7.1055
+\endauxfile
+
*/
//+ENDPLUMEDOC
diff --git a/src/ves/TD_LinearCombination.cpp b/src/ves/TD_LinearCombination.cpp
index 40f45416333cfc6be2411db8c4a92072721d113d..1ace9a5226fbfe82f620248a6caef227a70146e2 100644
--- a/src/ves/TD_LinearCombination.cpp
+++ b/src/ves/TD_LinearCombination.cpp
@@ -75,7 +75,7 @@ td_uni: TD_UNIFORM
td_gauss: TD_GAUSSIAN CENTER1=-2.0 SIGMA1=0.5
-td_comb: TD_LINEAR_COMBINATION DISTRIBUTIONS=td_uniform,td_gaussian
+td_comb: TD_LINEAR_COMBINATION DISTRIBUTIONS=td_uni,td_gauss
\endplumedfile
Here we employ a linear combination of a uniform and two Gaussian distribution.
diff --git a/src/ves/TD_ProductDistribution.cpp b/src/ves/TD_ProductDistribution.cpp
index 254b581739a5cfed2b0227a97c66628f53600d82..1310d84ac54520e336e15655332d4a63409511d5 100644
--- a/src/ves/TD_ProductDistribution.cpp
+++ b/src/ves/TD_ProductDistribution.cpp
@@ -69,7 +69,7 @@ argument 1 and a Gaussian distribution for argument 2.
\plumedfile
target_uniform: TD_UNIFORM
-target_Gaussian: TD_GAUSSIAN CENTER=-2.0 SIGMA=0.5
+target_Gaussian: TD_GAUSSIAN CENTER1=-2.0 SIGMA1=0.5
td_pd: TD_PRODUCT_DISTRIBUTION DISTRIBUTIONS=target_uniform,target_Gaussian
\endplumedfile
diff --git a/src/ves/TD_Uniform.cpp b/src/ves/TD_Uniform.cpp
index 3c0ccebbb4cdd83278a3f6318b1df30831e7799b..9fa9a568b774f2ad46e6e4abd0667135019e59f8 100644
--- a/src/ves/TD_Uniform.cpp
+++ b/src/ves/TD_Uniform.cpp
@@ -113,7 +113,7 @@ td: TD_UNIFORM
\endplumedfile
\plumedfile
TD_UNIFORM ...
- MINIMA=0.0,0,2
+ MINIMA=0.0,0.2
MAXIMA=10.0,1.0
LABEL=td
... TD_UNIFORM
diff --git a/user-doc/.gitignore b/user-doc/.gitignore
index 139073b02272c2415c636c5cdc237623e24a8bf1..656ae7430795e88b621d8a50c2420f1972dd622c 100644
--- a/user-doc/.gitignore
+++ b/user-doc/.gitignore
@@ -11,4 +11,4 @@
/manual.pdf
/regtests
/spelling
-
+/example-check
diff --git a/user-doc/Analysis.md b/user-doc/Analysis.md
index b3b602218fcdef4470c05b8226bd077f708c566f..2a45985ec126c5ddb06236ab64b6ac877763f25a 100644
--- a/user-doc/Analysis.md
+++ b/user-doc/Analysis.md
@@ -171,10 +171,13 @@ that are available in PLUMED are as follows
In general most of these landmark selection algorithms must be used in tandem with a \ref dissimilaritym "dissimilarity matrix" object as as follows:
\plumedfile
-data: COLLECT_FRAMES ARG=d1 STRIDE=1
+d1: DISTANCE ATOMS=1,2
+d2: DISTANCE ATOMS=3,4
+d3: DISTANCE ATOMS=5,6
+data: COLLECT_FRAMES ARG=d1,d2,d3 STRIDE=1
ss1: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=data
ll2: LANDMARK_SELECT_FPS USE_OUTPUT_DATA_FROM=ss1 NLANDMARKS=300
-OUTPUT_COLVAR_FILE USE_OUTPUT_DATA_FROM=ll2 FILE=mylandmarks
+OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=ll2 FILE=mylandmarks
\endplumedfile
When landmark selection is performed in this way a weight is ascribed to each of the landmark configurations. This weight is
@@ -208,7 +211,10 @@ the following <a href="https://www.youtube.com/watch?v=ofC2qz0_9_A&feature=youtu
Within PLUMED running an input to run a dimensionality reduction algorithm can be as simple as:
\plumedfile
-data: COLLECT_FRAMES STRIDE=1 ARG=d1
+d1: DISTANCE ATOMS=1,2
+d2: DISTANCE ATOMS=3,4
+d3: DISTANCE ATOMS=5,6
+data: COLLECT_FRAMES STRIDE=1 ARG=d1,d2,d3
ss1: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=data
mds: CLASSICAL_MDS USE_OUTPUT_DATA_FROM=ss1 NLOW_DIM=2
\endplumedfile
@@ -217,11 +223,14 @@ Where we have to use the \ref EUCLIDEAN_DISSIMILARITIES action here in order to
We can even throw some landmark selection into this procedure and perform
\plumedfile
-data: COLLECT_FRAMES STRIDE=1 ARG=d1
+d1: DISTANCE ATOMS=1,2
+d2: DISTANCE ATOMS=3,4
+d3: DISTANCE ATOMS=5,6
+data: COLLECT_FRAMES STRIDE=1 ARG=d1,d2,d3
matrix: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=data
ll2: LANDMARK_SELECT_FPS USE_OUTPUT_DATA_FROM=matrix NLANDMARKS=300
mds: CLASSICAL_MDS USE_OUTPUT_DATA_FROM=ll2 NLOW_DIM=2
-osample: PROJECT_ALL_ANALYSIS_DATA USE_OUTPUT_DATA_FROM=matrix PROJECTION=smap
+osample: PROJECT_ALL_ANALYSIS_DATA USE_OUTPUT_DATA_FROM=matrix PROJECTION=mds
\endplumedfile
Notice here that the final command allows us to calculate the projections of all the non-landmark points that were collected by the action with
diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile
index b14c707d92afaffdc06139d9f991c305f20b835f..7844b91fb905f8b38a2401261097deacab0a7f10 100644
--- a/user-doc/Doxyfile
+++ b/user-doc/Doxyfile
@@ -238,6 +238,12 @@ ALIASES = \
"tarball{1}=\htmlonly<span style=\"background-color:yellow\">\endhtmlonly<a href=\"tutorial-resources/\1.tar.gz\" style=\"font-weight:bold\" style=\"color:green\" download=\"\1.tar.gz\"> TARBALL </a>\htmlonly</span>\endhtmlonly" \
"plumedfile=\verbatim BEGIN_PLUMED_FILE" \
"endplumedfile=\endverbatim" \
+ "plumedmultireplicafile{1}=\verbatim BEGIN_PLUMED_FILE" \
+ "endplumedmultireplicafile=\endverbatim" \
+ "plumedincludefile=\verbatim BEGIN_PLUMED_FILE" \
+ "endplumedincludefile=\endverbatim" \
+ "auxfile{1}=\verbatim" \
+ "endauxfile=\endverbatim" \
"plumednotmaintained=\warning This branch is not maintained. Users are invited to upgrade to a newer version"
# This tag can be used to specify a number of word-keyword mappings (TCL only).
diff --git a/user-doc/Files.md b/user-doc/Files.md
index 78e8254a8e1617237856cb30b2c42b009e31989a..b2cc353cb3e18cfeeba8afcf9fb0be5afb6d5a75 100644
--- a/user-doc/Files.md
+++ b/user-doc/Files.md
@@ -54,7 +54,7 @@ This means that using in a multi-replica context an input such as
\plumedfile
d: DISTANCE ATOMS=1,2
PRINT ARG=d FILE=COLVAR.gz
-METAD ARG=d FILE=test.HILLS SIGMA=0.1 HEIGHT=0.1
+METAD ARG=d FILE=test.HILLS SIGMA=0.1 HEIGHT=0.1 PACE=100
\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
diff --git a/user-doc/Miscelaneous.md b/user-doc/Miscelaneous.md
index d53c840e2f675a81e2c1fd554f2bffd73e9758a2..9978e59f129208f60bf1a761cc9a4765395cdb90 100644
--- a/user-doc/Miscelaneous.md
+++ b/user-doc/Miscelaneous.md
@@ -471,13 +471,14 @@ RESTRAINT ARG=dist
could be split up into two files as shown below:
\plumedfile
-DISTANCE ATOMS=0,1 LABEL=dist
-INCLUDE FILE=toBeIncluded.dat
-\endplumedfile
-plus a "toBeIncluded.dat" file
-\plumedfile
-RESTRAINT ARG=dist
+DISTANCE ATOMS=1,2 LABEL=dist
+INCLUDE FILE=toBeIncluded.inc
\endplumedfile
+plus a "toBeIncluded.inc" file
+\plumedincludefile
+# this is toBeIncluded.inc
+RESTRAINT ARG=dist AT=2.0 KAPPA=1.0
+\endplumedincludefile
However, when you do this it is important to recognize 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
@@ -529,7 +530,7 @@ file with common definitions and specific input files with replica-dependent key
However, as of PLUMED 2.4, we introduced a simpler manner to manipulate multiple replica
inputs with tiny differences. Look at the following example:
-\plumedfile
+\plumedmultireplicafile{3}
# Compute a distance
d: DISTANCE ATOMS=1,2
@@ -541,7 +542,7 @@ RESTRAINT ARG=d AT=@replicas:1.0,1.1,1.2 KAPPA=1.0
# RESTRAINT ARG=d AT=1.1 KAPPA=1.0
# On replica 2, this means:
# RESTRAINT ARG=d AT=1.2 KAPPA=1.0
-\endplumedfile
+\endplumedmultireplicafile
If you prepare a single `plumed.dat` file like this one and feeds it to PLUMED while using 3 replicas,
the 3 replicas will see the very same input except for the `AT` keyword, that sets the position of the restraint.
@@ -549,7 +550,7 @@ Replica 0 will see a restraint centered at 1.0, replica 1 centered at 1.1, and r
The `@replicas:` keyword is not special for \ref RESTRAINT or for the `AT` keyword. Any keyword in PLUMED can accept that syntax.
For instance, the following single input file can be used to setup a bias exchange metadynamics \cite piana simulations:
-\plumedfile
+\plumedmultireplicafile{2}
# Compute distance between atoms 1 and 2
d: DISTANCE ATOMS=1,2
@@ -569,7 +570,7 @@ METAD ...
# METAD ARG=d HEIGHT=1.0 PACE=100 SIGMA=0.1 GRID_MIN=0.0 GRID_MAX=2.0
# On replica 1, this means:
# METAD ARG=t HEIGHT=1.0 PACE=100 SIGMA=0.3 GRID_MIN=-pi GRID_MAX=+pi
-\endplumedfile
+\endplumedmultireplicafile
This would be a typical setup for a bias exchange simulation.
Notice that even though variables `d` and `t` are both read in both replicas,
@@ -579,7 +580,7 @@ This is because variables that are defined but not used are never actually calcu
If the value that should be provided for each replica is a vector, you should use curly braces as delimiters.
For instance, if the restraint acts on two variables, you can use the following input:
-\plumedfile
+\plumedmultireplicafile{3}
# Compute distance between atoms 1 and 2
d: DISTANCE ATOMS=10,20
@@ -598,13 +599,13 @@ RESTRAINT ...
# RESTRAINT ARG=d AT=3.0,4.0 KAPPA=1.0,3.0
# On replica 2 this means:
# RESTRAINT ARG=d AT=5.0,6.0 KAPPA=1.0,3.0
-\endplumedfile
+\endplumedmultireplicafile
Notice the double curly braces. The outer ones are used by PLUMED to know there the argument of the `AT` keyword ends,
whereas the inner ones are used to group the values corresponding to each replica.
Also notice that the last example can be split in multiple lines exploiting the fact that
within multi-line statements (enclosed by pairs of `...`) newlines are replaced with simple spaces:
-\plumedfile
+\plumedmultireplicafile{3}
d: DISTANCE ATOMS=10,20
t: TORSION ATOMS=30,31,32,33
RESTRAINT ...
@@ -616,9 +617,9 @@ RESTRAINT ...
{3.0,4.0}
{5.0,6.0}
}
- KAPPA=1.0
+ KAPPA=1.0,3.0
...
-\endplumedfile
+\endplumedmultireplicafile
In short, whenever there are keywords that should vary across replicas, you should set them using the `@replicas:` keyword.
As mentioned above, you can always use the old syntax with separate input file, and this is recommended when the
diff --git a/user-doc/Performances.md b/user-doc/Performances.md
index 20c0fb984e83094b599ebe3b7e932c1dda095605..e9ff663bb3f144a219065de5e63658ee40b94d28 100644
--- a/user-doc/Performances.md
+++ b/user-doc/Performances.md
@@ -274,12 +274,10 @@ make install
You are done!
In some case using a custom expression is almost as fast as using a hard-coded
-function. For instance, with an input like this one:
+function. For instance, with an input that contained the following lines:
\plumedfile
-...
c: COORDINATION GROUPA=1-108 GROUPB=1-108 R_0=1
d_fast: COORDINATION GROUPA=1-108 GROUPB=1-108 SWITCH={CUSTOM FUNC=1/(1+x2^3) R_0=1}
-...
\endplumedfile
I (GB) obtained the following timings (on a Macbook laptop):
\verbatim
diff --git a/user-doc/figs/lugano-5-gismo.png b/user-doc/figs/lugano-5-gismo.png
new file mode 100644
index 0000000000000000000000000000000000000000..d1c3bc5274332d4d71f590ec97a2b316e5949d2c
Binary files /dev/null and b/user-doc/figs/lugano-5-gismo.png differ
diff --git a/user-doc/figs/lugano-6d-gb.png b/user-doc/figs/lugano-6d-gb.png
new file mode 100644
index 0000000000000000000000000000000000000000..d974b6aa9c0a07ee83c231841965aaf66029bcb6
Binary files /dev/null and b/user-doc/figs/lugano-6d-gb.png differ
diff --git a/user-doc/figs/lugano-2-pca-coordinates.png b/user-doc/figs/marvel-2-pca-coordinates.png
similarity index 100%
rename from user-doc/figs/lugano-2-pca-coordinates.png
rename to user-doc/figs/marvel-2-pca-coordinates.png
diff --git a/user-doc/figs/lugano-2-trans-state.png b/user-doc/figs/marvel-2-trans-state.png
similarity index 100%
rename from user-doc/figs/lugano-2-trans-state.png
rename to user-doc/figs/marvel-2-trans-state.png
diff --git a/user-doc/go-example-check b/user-doc/go-example-check
new file mode 100755
index 0000000000000000000000000000000000000000..5fd360d9b13461fa610d003d63e92d687bedc6c4
--- /dev/null
+++ b/user-doc/go-example-check
@@ -0,0 +1,171 @@
+#!/bin/bash
+
+rm -rf example-check
+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
+ # Single replica examples
+ splits=`echo $file | sed -e 's/\// /g'`
+ nf=`echo $splits | awk '{print NF}'`
+ fname=`echo $splits | awk -v n=$nf '{print $n}'`
+ cat $file |
+ awk 'BEGIN{inp=0;}{
+ if( $1=="\\endplumedfile" ){ print ">>END OF EXAMPLE>>"; inp=0; }
+ else if( $1=="\\plumedfile" ){ inp=1; }
+ else if( inp==1 ){ print $0; }
+ }' > example-check/$fname.dat
+ # Multiple replica examples
+ splits=`echo $file | sed -e 's/\// /g'`
+ nf=`echo $splits | awk '{print NF}'`
+ fname=`echo $splits | awk -v n=$nf '{print $n}'`
+ cat $file |
+ awk 'BEGIN{inp=0;}{
+ if( $1=="\\endplumedmultireplicafile" ){ print ">>END OF EXAMPLE>>"; inp=0; }
+ else if( match($1,"plumedmultireplicafile") ){ inp=1; print "# " $0 }
+ else if( inp==1 ){ print $0; }
+ }' >> example-check/$fname.dat
+ #Â Count the number of examples found in the input
+ neg=`grep ">>END OF EXAMPLE>>" example-check/$fname.dat | wc -l | awk '{print $1}'`
+ if [ $neg -gt 0 ] ; then
+ # Make a directory to hold all the inputs
+ mkdir example-check/$fname
+ #Â Now split the examples found into the set of example input files in the documentation
+ sline=0
+ for ((i=1;i<=$neg;++i)) ; do
+ eline=`grep -n ">>END OF EXAMPLE>>" example-check/$fname.dat | head -n $i | tail -n 1 | awk '{print $1}' | sed -e 's/:>>END//g'`
+ head -n $(($eline-1)) example-check/$fname.dat | tail -n $(($eline-1-$sline)) > example-check/$fname/$i.dat
+ wrongc=`grep "this is wrong" example-check/$fname/$i.dat | wc -l | awk '{print $1}'`
+ if [ $wrongc -gt 0 ] ; then
+ rm example-check/$fname/$i.dat
+ fi
+ sline=$eline
+ done
+ # Check for plumed include files
+ cat $file |
+ awk 'BEGIN{inp=0;}{
+ if( $1=="\\endplumedincludefile" ){ print ">>END OF EXAMPLE>>"; inp=0; }
+ else if( $1=="\\plumedincludefile" ){ inp=1; }
+ else if( inp==1 ){ print $0; }
+ }' > example-check/$fname.inc
+ ninc=`grep ">>END OF EXAMPLE>>" example-check/$fname.inc | wc -l | awk '{print $1}'`
+ # And split the set of include files
+ sline=0
+ for ((i=1;i<=$ninc;++i)) ; do
+ checks=`grep -A 1 "plumedincludefile" $file | head -n $((($i-1)*6+2)) | tail -n 1 | awk '{match($0,"# this is")}'`
+ ifname=`grep -A 1 "plumedincludefile" $file | head -n $((($i-1)*6+2)) | tail -n 1 | awk '{if(match($0,"# this is")){ print $4; } else { print "ERROR";}}'`
+ if [ $ifname == "ERROR" ] ; then
+ echo ERROR in specification of include file for $file
+ exit 1
+ fi
+ eline=`grep -n ">>END OF EXAMPLE>>" example-check/$fname.inc | head -n $i | tail -n 1 | awk '{print $1}' | sed -e 's/:>>END//g'`
+ head -n $(($eline-1)) example-check/$fname.inc | tail -n $(($eline-1-$sline)) > example-check/$fname/$ifname
+ sline=$eline
+ done
+ rm example-check/$fname.inc
+ # Check for auxiliary files
+ cat $file |
+ awk 'BEGIN{inp=0;}{
+ if( $1=="\\endauxfile" ){ print ">>END OF EXAMPLE>>"; inp=0; }
+ else if( match($1,"\\auxfile") ){ inp=1; }
+ else if( inp==1 ){ print $0; }
+ }' > example-check/$fname.aux
+ naux=`grep ">>END OF EXAMPLE>>" example-check/$fname.aux | wc -l | awk '{print $1}'`
+ # And split the set of include files
+ sline=0
+ for ((i=1;i<=$naux;++i)) ; do
+ ifname=`grep "auxfile" $file | grep -v "endauxfile" | head -n $i | tail -n 1 | sed -e 's/\\\auxfile{//' | sed -e 's/}//'`
+ eline=`grep -n ">>END OF EXAMPLE>>" example-check/$fname.aux | head -n $i | tail -n 1 | awk '{print $1}' | sed -e 's/:>>END//g'`
+ head -n $(($eline-1)) example-check/$fname.aux | tail -n $(($eline-1-$sline)) > example-check/$fname/$ifname
+ sline=$eline
+ done
+ rm example-check/$fname.aux
+ fi
+ rm example-check/$fname.dat
+done
+
+# Copy the data directories needed for CS2BACKBONE so we can run these tests
+cp -pr ../regtest/isdb/rt-cs2backbone/data example-check/CS2BACKBONE.txt/data
+# Change to the directory that contains the examples that we are testing
+cd example-check
+
+# These are things that are not really input files and that are expected to never work
+rm -f MiscelaneousPP.md/10.dat MiscelaneousPP.md/11.dat
+# These are things that we might want to fix
+rm -rf PLUMED.txt
+
+# Here we have a list of things that are currently not working. We delete the input files for these
+# so as to avoid them causing problems. As they are fixed we will reincorporate them and delete these lines
+rm -rf FUNCPATHMSD.txt/3.dat PIV.txt # This is all PIV
+# This is stuff for Gareth to work on
+rm -rf FOURIER_TRANSFORM.txt
+# These are problems that Max and Carlo need to fix
+rm -rf NOE.txt SAXS.txt RDC.txt LOCALENSEMBLE.txt EEFSOLV.txt EMMI.txt METAINFERENCE.txt/2.dat
+# These are problems for Giovanni to fix
+rm -rf PIECEWISE.txt PUCKERING.txt/ MiscelaneousPP.md/19.dat
+# These are things for Omar to fix
+rm -rf VES_OUTPUT_FES.txt/ VES_LINEAR_EXPANSION.txt/
+# Not sure how to get this to work - won't compile on my laptop GAT
+rm -rf DRR.txt
+# Stuff in tutorials that doesn't quite work
+rm -f a-trieste-6.txt/1.dat a-trieste-6.txt/2.dat
+rm -rf isdb-1.txt isdb-2.txt performance-optimization.txt
+rm -rf ves-lugano2017-02-ves1.txt ves-lugano2017-03-ves2.txt ves-lugano2017-04-kinetics.txt
+
+# Now check that plumed can parse all the inputs in the manual
+for dir in * ; do
+ cd $dir
+ for file in *.dat ; do
+ echo Checking example named $dir/$file
+ # This checks if we need a structure file for a MOLINFO command and gets one if it is required
+ 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
+ fi
+ fi
+
+ # Now running test with PLUMED
+ nsnip=`grep snip $file | wc -l | awk '{print $1}'`
+ nload=`grep "LOAD" $file | wc -l | awk '{print $1}'`
+ # Want to get rid of these
+ ntarget=`grep "TARGET=" $file | wc -l | awk '{print $1}'`
+ if [ $nsnip -eq 0 ] && [ $nload -eq 0 ] && [ $nfill -eq 0 ] ; then
+ hasrep=`grep plumedmultireplicafile $file | wc -l | awk '{print $1}'`
+ if [ $hasrep -gt 0 ] ; then
+ nrep=`grep plumedmultireplicafile $file | awk '{print $2}' | sed -e 's/\\\plumedmultireplicafile{//' | sed -e 's/}//'`
+ mpirun -np $nrep ../../../src/lib/plumed driver --natoms 100000 --parse-only --kt 2.49 --plumed $file --multi $nrep > check.log
+ else
+ ../../../src/lib/plumed driver --natoms 100000 --parse-only --kt 2.49 --plumed $file > check.log
+ fi
+ nerr=`grep "PLUMED error" check.log | wc -l | awk '{print $1}'`
+ if [ $nerr -gt 0 ] ; then
+ echo Found mistakes for examples $file
+ cat check.log
+ exit 1
+ fi
+ elif [ $nload -gt 0 ] ; then
+ echo WARNING: FILE named $dir/$file tries to LOAD external functionality
+ elif [ $nfill -gt 0 ] ; then
+ echo ERROR: File named $dir/$file contains a FILL statement
+ else
+ echo ERROR: File named $dir/$file contains a snip
+ fi
+ done
+ cd ../
+done
+
+# Remove some crap that is created somewhere
+cd ../
diff --git a/user-doc/tutorials/a-trieste-1.txt b/user-doc/tutorials/a-trieste-1.txt
index 0b20d690aba6fc5fe0ce5c967d5621bddaabb314..9f1b376503e6b97c4e80342646f813b4b18641b8 100644
--- a/user-doc/tutorials/a-trieste-1.txt
+++ b/user-doc/tutorials/a-trieste-1.txt
@@ -263,7 +263,7 @@ d2: DISTANCE ATOMS=1,3
d3: DISTANCE ATOMS=1,4
# Compute the sum of the squares of those three distances:
-c: COMBINE ARG=d1,d2,d3 POWERS=2 PERIODIC=NO
+c: COMBINE ARG=d1,d2,d3 POWERS=2,2,2 PERIODIC=NO
# Sort the three distances:
s: SORT ARG=d1,d2,d3
diff --git a/user-doc/tutorials/a-trieste-2.txt b/user-doc/tutorials/a-trieste-2.txt
index 51e4bc0d5d74b91881d5a8c10a2330800f376f92..2ec2322025cd85247b1a363f278932276495c5a8 100644
--- a/user-doc/tutorials/a-trieste-2.txt
+++ b/user-doc/tutorials/a-trieste-2.txt
@@ -105,7 +105,17 @@ Copy the contents of the box above to a plain text file called generate_data.py,
> python generate_data.py > my_data
\endverbatim
-This will generate a file called my_data that contains 10001 uniform random variables. PLUMED will ignore the first number in the colvar file as it assumes
+This will generate a file called my_data that contains 10001 uniform random variables. The first few lines of this file should look something like this:
+
+\auxfile{my_data}
+#! FIELDS time rand
+0 0.7880696770414992
+1 0.6384371499082688
+2 0.01373858851099563
+3 0.30879241147755776
+\endauxfile
+
+PLUMED will ignore the first number in the colvar file as it assumes
this is the initial configuration you provided for the trajectory. The sample mean will thus be calculated from 10000 random variables. Plot this data now
using gnuplot and the command:
@@ -322,6 +332,16 @@ Copy the script above to a file called gen-normal.py and then execute the python
> python gen-normal.py > mynormal
\endverbatim
+This should produce a file called mynormal. The first few lines of this file will look something like the following:
+
+\auxfile{mynormal}
+#! FIELDS time rand
+0 0.7216627600374712
+1 0.7460765782434674
+2 0.7753011891527442
+3 0.5643419178297695
+\endauxfile
+
<b>
Use what you have learned from the exercises above to estimate the ensemble average from these generated data points using PLUMED. If you want
you can use block averaging but it does not matter if you do it by just considering all the data in the input file. What would you expect the ensemble average
@@ -431,6 +451,15 @@ Copy the python script above to a filled called correlated-data.py and then exec
> python correlated-data.py > mycorr
\endverbatim
+This should output a file called mycorr. The first few lines of this file should look something like the following:
+
+\auxfile{mycorr}
+#! FIELDS time rand
+0 0.17818391042061332
+1 0.33368077871483476
+2 0.0834749323925259
+\endauxfile
+
The autocorrelation function, \f$R(\tau)\f$ provides a simple method for determining whether or not there are correlations between the random variables, \f$X\f$,
in our time series. This function is defined as follows:
@@ -456,7 +485,7 @@ the analysis with PLUMED and explain the results that we get at each stage of th
distribution using the following PLUMED input:
\plumedfile
-data: READ FILE=my_data VALUES=rand
+data: READ FILE=mycorr VALUES=rand
av5: AVERAGE ARG=data STRIDE=1 CLEAR=5
PRINT ARG=av5 FILE=colvar5 STRIDE=5
av10: AVERAGE ARG=data STRIDE=1 CLEAR=10
@@ -589,7 +618,17 @@ Copy this script to a filled called do-monte-carlo.py and execute the contents o
\endverbatim
This will run a short Monte Carlo simulation that generates (time-correlated) random data from a (roughly) Gaussian distribution by attempting
-random translational moves of up to 0.1 units. An autocorrelation function that was calculated
+random translational moves of up to 0.1 units. The command above will generate a file called mcdata the first few lines of which should look
+somethign like the following:
+
+\auxfile{mcdata}
+#! FIELDS time rand
+0 0.17818391042061332
+1 0.33368077871483476
+2 0.0834749323925259
+\endauxfile
+
+An autocorrelation function that was calculated
using data generated using this script is shown below. You can clearly see from this figure that there are correlations between
the adjacent data points in the time series and that we have to do block averaging as a result.
diff --git a/user-doc/tutorials/a-trieste-5.txt b/user-doc/tutorials/a-trieste-5.txt
index 445f3b94f22c7d9ee6b99b0e1fe0aff82fc68d4c..17d39dec961813ba945b081963d587e3e0f50c2b 100644
--- a/user-doc/tutorials/a-trieste-5.txt
+++ b/user-doc/tutorials/a-trieste-5.txt
@@ -103,7 +103,7 @@ file with common definitions and specific input files with replica-dependent key
However, as of PLUMED 2.4, we introduced a simpler manner to manipulate multiple replica
inputs with tiny differences. Look at the following example:
-\plumedfile
+\plumedmultireplicafile{3}
# Compute a distance
d: DISTANCE ATOMS=1,2
@@ -115,7 +115,7 @@ RESTRAINT ARG=d AT=@replicas:1.0,1.1,1.2 KAPPA=1.0
# RESTRAINT ARG=d AT=1.1 KAPPA=1.0
# On replica 2, this means:
# RESTRAINT ARG=d AT=1.2 KAPPA=1.0
-\endplumedfile
+\endplumedmultireplicafile
If you prepare a single `plumed.dat` file like this one and feeds it to PLUMED while using 3 replicas,
the 3 replicas will see the very same input except for the `AT` keyword, that sets the position of the restraint.
@@ -123,7 +123,7 @@ Replica 0 will see a restraint centered at 1.0, replica 1 centered at 1.1, and r
The `@replicas:` keyword is not special for \ref RESTRAINT or for the `AT` keyword. Any keyword in PLUMED can accept that syntax.
For instance, the following single input file can be used to setup a bias exchange metadynamics \cite piana simulations:
-\plumedfile
+\plumedmultireplicafile{2}
# Compute distance between atoms 1 and 2
d: DISTANCE ATOMS=1,2
@@ -143,7 +143,7 @@ METAD ...
# METAD ARG=d HEIGHT=1.0 PACE=100 SIGMA=0.1 GRID_MIN=0.0 GRID_MAX=2.0
# On replica 1, this means:
# METAD ARG=t HEIGHT=1.0 PACE=100 SIGMA=0.3 GRID_MIN=-pi GRID_MAX=+pi
-\endplumedfile
+\endplumedmultireplicafile
This would be a typical setup for a bias exchange simulation.
Notice that even though variables `d` and `t` are both read in both replicas,
@@ -153,7 +153,7 @@ This is because variables that are defined but not used are never actually calcu
If the value that should be provided for each replica is a vector, you should use curly braces as delimiters.
For instance, if the restraint acts on two variables, you can use the following input:
-\plumedfile
+\plumedmultireplicafile{3}
# Compute distance between atoms 1 and 2
d: DISTANCE ATOMS=10,20
@@ -172,13 +172,13 @@ RESTRAINT ...
# RESTRAINT ARG=d AT=3.0,4.0 KAPPA=1.0,3.0
# On replica 2 this means:
# RESTRAINT ARG=d AT=5.0,6.0 KAPPA=1.0,3.0
-\endplumedfile
+\endplumedmultireplicafile
Notice the double curly braces. The outer ones are used by PLUMED to know there the argument of the `AT` keyword ends,
whereas the inner ones are used to group the values corresponding to each replica.
Also notice that the last example can be split in multiple lines exploiting the fact that
within multi-line statements (enclosed by pairs of `...`) newlines are replaced with simple spaces:
-\plumedfile
+\plumedmultireplicafile{3}
d: DISTANCE ATOMS=10,20
t: TORSION ATOMS=30,31,32,33
RESTRAINT ...
@@ -192,7 +192,7 @@ RESTRAINT ...
}
KAPPA=1.0
...
-\endplumedfile
+\endplumedmultireplicafile
In short, whenever there are keywords that should vary across replicas, you should set them using the `@replicas:` keyword.
As mentioned above, you can always use the old syntax with separate input file, and this is recommended when the
diff --git a/user-doc/tutorials/aa-lugano-1.txt b/user-doc/tutorials/aa-lugano-1.txt
index 444f664339905bd1cf6f81b96349dddd22c7549f..b56d58fa117a8d6cf3d7028776ae3e434385af84 100644
--- a/user-doc/tutorials/aa-lugano-1.txt
+++ b/user-doc/tutorials/aa-lugano-1.txt
@@ -314,7 +314,7 @@ the GB1 protein:
- traj-broken.xtc: the original GROMACS trajectory in which GB1 is broken by periodic boundary conditions
- traj-whole.xtc: the trajectory processed by the `gmx trjconv` utility to fix PBCs discontinuities
-In many PLUMED CVs, PBCs are automatically taken into account unless a special option (\ref NOPBC) is used.
+In many PLUMED CVs, PBCs are automatically taken into account unless a special option (NOPBC) is used.
In this way, the user can work directly with the raw trajectory `traj-broken.xtc`.
Alternatively, PLUMED can reconstruct internally the coordinates of the system and thus fix discontinuities due to PBCs.
In order to do so, the \ref WHOLEMOLECULES action should be used.
@@ -465,5 +465,3 @@ and then check that the custom CVs are indeed what they are expected by plotting
link: @subpage lugano-1
description: This tutorial explains the syntax of the PLUMED input file and how to use PLUMED to analyze CVs
-
-additional-files: lugano-1
diff --git a/user-doc/tutorials/aa-lugano-2.txt b/user-doc/tutorials/aa-lugano-2.txt
index 2ad02c8051aaf945992977ff18bc38ba2b7c0351..9fef70f06351311700b1583a8c39eea8c46c6acf 100644
--- a/user-doc/tutorials/aa-lugano-2.txt
+++ b/user-doc/tutorials/aa-lugano-2.txt
@@ -414,7 +414,7 @@ restraint-phi: RESTRAINT ...
PRINT STRIDE=20 ARG=phi,psi,restraint-phi.bias FILE=COLVAR
\endplumedfile
-The @replicas syntax allow to define different values for a variable for the different replicas.
+The \@replicas syntax allow to define different values for a variable for the different replicas.
\verbatim
mpiexec -np 25 gmx_mpi -s topol -plumed plumed.dat -multi 25 -replex 100 -nb cpu -nsteps 100000
diff --git a/user-doc/tutorials/aa-lugano-4.txt b/user-doc/tutorials/aa-lugano-4.txt
index 5e5ec3b4f291506fb6a045f50f93562f999fa74c..bc343abfd39ba433d547f00e9798dcc78ae0c84d 100644
--- a/user-doc/tutorials/aa-lugano-4.txt
+++ b/user-doc/tutorials/aa-lugano-4.txt
@@ -136,7 +136,7 @@ To prevent the cluster from evaporating you need to lower the temperature in the
<b>
Now try to think how we can use a bias potential to stop the cluster from evaporating. Why might using a bias potential be preferable to the method that you have just employed?
N.B. The next exercise is in the hidden section below so you need to expand it. Please try to come up with your own answer to the question of what bias potential we should be using
-before expanding this section by thinking about the material that was covered in \ref a-lugano-2.
+before expanding this section by thinking about the material that was covered in \ref lugano-2.
</b>
\hidden{The bias potential}
diff --git a/user-doc/tutorials/aa-lugano-6b.txt b/user-doc/tutorials/aa-lugano-6b.txt
index 06262ac153a33962f5259d5f4c33620a8f7bea2f..e6d1084857ceaef299b85ae30222fa7f01877728 100644
--- a/user-doc/tutorials/aa-lugano-6b.txt
+++ b/user-doc/tutorials/aa-lugano-6b.txt
@@ -31,12 +31,12 @@ no internal degree of freedom, and instead of a protein with a complex binding p
We are also assuming to know which is the proper binding site, since we can easily guess that the most stable binding will
happen on the phosphate.
-\section lugano-6a-exercises Exercises
+\section lugano-6b-exercises Exercises
*/
-link: @subpage lugano-6a
+link: @subpage lugano-6b
-description: An exercise on running PLUMED with LAMMPS
+description: An exercise to compute binding free energies
-additional-files: lugano-6a
+additional-files: lugano-6b
diff --git a/user-doc/tutorials/aa-lugano-6c.txt b/user-doc/tutorials/aa-lugano-6c.txt
new file mode 100644
index 0000000000000000000000000000000000000000..95262549faeb0203e89ebec5941587d9765382e9
--- /dev/null
+++ b/user-doc/tutorials/aa-lugano-6c.txt
@@ -0,0 +1,74 @@
+/**
+\page lugano-6c Lugano tutorial: Computing proton transfer in water
+
+\section lugano-6c-aim Aims
+
+In this tutorial I will show you how you can use PLUMED and metadynamics in combinations with CP2K.
+
+\section lugano-6c-lo Objectives
+
+Once this tutorial is completed students will
+
+- Know how to enhance the sampling in an ab initio simulation.
+
+\section lugano-6c-resources Resources
+
+The \tarball{lugano-6c} for this project contains the following files:
+
+- H-transfer.inp: a CP2K input file to perform BO-MD and Free Energy calculations with PLUMED
+- H-transfer.pdb: a PDB file with the starting configuration for a few water molecules
+
+This tutorial has been tested on v2.5 but it should also work with other versions of PLUMED.
+
+\section lugano-6c-intro Introduction
+
+For this tutorial we will consider a practical application. The aim is that of studying proton transfer in water.
+The system is simplified and the accuracy of the ab initio simulation is not production like so do not reuse the
+CP2K input for real-life applications.
+
+\section lugano-6c-exercises Exercises
+
+In this example the system is initially in a configuration where there are H3O+ and an OH- molecule separated by a few
+other water molecules. In a standard MD the system will quickly equilbrate. Here the aim is to use metadynamics to estimate
+the free energy of this process and to understand the role of the solvent.
+
+CP2K includes natively the interface for PLUMED but it must be compiled using the proper flags, check CP2K installation instructions.
+
+
+\section lugano-6c-ex-1 Exercise 1: Preliminary run
+
+The starting configuration is represented in the H-transfer.pdb. While a simple CP2K input file to perform BO-MD is written in
+H-transfer.inp. In particular here the section to enable PLUMED is commented out initially.
+
+\verbatim
+# &FREE_ENERGY
+# &METADYN
+# USE_PLUMED .TRUE.
+# PLUMED_INPUT_FILE ./plumed.dat
+# &END METADYN
+# &END FREE_ENERGY
+\endverbatim
+
+To run a prelimnary simulation it is enough to:
+
+\verbatim
+cp2k.sopt H-transfer.inp >& log &
+\endverbatim
+
+use the plumed \ref driver and VMD to choose to water molecule relatively far apart to study the proton transfer.
+
+\section lugano-6c-ex-2 Exercise 2: Proton transfer
+
+In this exercise you are challanged to
+- Select two water molecule to be kept far apart using UPPER_WALLS and the distance between their two oxygen atoms.
+- Use the distances of an hydrogen from both oxygens to setup a first \ref METAD calculation to study the proton transfer between the selected water molecules
+- Test more complex CVs maybe taking into accout the role of the other molecules.
+- Think how to study proton transfer in a general way instead than between two specif water molecules and using a specific hydrongen.
+
+*/
+
+link: @subpage lugano-6c
+
+description: An exercise to run a simple proton transfer calculation with CP2K
+
+additional-files: lugano-6c
diff --git a/user-doc/tutorials/aa-lugano-6d.txt b/user-doc/tutorials/aa-lugano-6d.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7dd93bf64cd9cf94844f1dad3e264805f3487c1a
--- /dev/null
+++ b/user-doc/tutorials/aa-lugano-6d.txt
@@ -0,0 +1,90 @@
+/**
+\page lugano-6d Lugano tutorial: Folding free energy for a protein described by a go-model
+
+\section lugano-6d-aims Aims
+
+The aim of this tutorial is to train users to
+learn the syntax of complex collective variables and use them to analyze
+MD trajectories of realistic biological systems and bias them with metadynamics.
+
+\section lugano-6d-objectives Objectives
+
+Once this tutorial is completed students will be able to:
+- Write the PLUMED input file to use complex CVs for analysis
+- Analyze trajectories and calculate the free energy of complex biological systems
+- Perform error analysis and evaluate convergence in realistic situations
+- Setup, run, and analyze metadynamics simulations of a complex system
+
+\section lugano-6d-resources Resources
+
+The \tarball{lugano-6d} for this tutorial contains the following files:
+- GB1.tpr: a GROMACS run file to perform MD simulation of GB1
+- GB1_native.pdb: a PDB file for the folded structure of GB1
+- GB1_smog.top: the GROMACS topology file
+- GB1.mdp: the gromacs simulation parameters file
+- GB1_start.gro: the starting configuration of the simulation
+
+\section lugano-6d-intro Introduction
+
+In this tutorial we propose exercises on the protein G B1 domain described using a structure-based potential obtained using SMOG (smog-server.org)
+
+\section lugano-6d-ex-1 Exercise 1: Protein G folding simulations
+GB1 is a small protein domain with a simple beta-alpha-beta fold. It is a well studied protein that folds on the millisecond time scale.
+Here we use a structure based potential and well-tempered metadynamics to study the free energy of folding and unfolding.
+In the TARBALL of this exercise we provide the files needed to run the simulation, the user should write the plumed input file needed
+to bias the sampling.
+
+\anchor lugano-6d-pgb
+\image html lugano-6d-gb.png "The crystal structure of the protein G B1 domain"
+
+The users are expected to:
+- setup and perform a well-tempered metadynamics simulation
+- evaluate convergence and error calculation of the metadynamics simulation
+- calculate the free energy difference between the folded and unfolded state of this protein
+- evaluate the robustness of the former by reweighting the resulting free energy as function of different CVs
+
+The users are free to choose his/her favorite CVs and they are encouraged to use the
+on-line manual to create their own PLUMED input file.
+However, we encourage all the users to experiment at least with the following CVs to characterize
+the free-energy landscape of GB1:
+
+- \ref RMSD with respect to the folded state
+- \ref DRMSD with respect to the folded state
+- \ref GYRATION
+- \ref ALPHABETA
+- \ref DIHCOR
+
+Unfortunately secondary structure collective variables cannot be used in this case because the model does not include hydrogens.
+
+The users should first perform a preliminary simulations and use this to select one or more CV to be later employed for a \ref METAD or \ref RESTRAINT (umbrella sampling) simulation.
+Once you are satisfied by the convergence of your simulation, you can use one of the reweighting algorithms proposed
+to evaluate the free-energy difference between folded and unfolded state as a function of multiple collective variables.
+
+\plumedfile
+#this allows you to use short-cut for dihedral angles
+MOLINFO STRUCTURE=GB1_native.pdb
+
+#add here the collective variables you want to bias
+
+#add here the RESTRAINT or METAD bias, remember that for METAD you need to set: one SIGMA per CV, one single HEIGHT, one BIASFACTOR and one PACE.
+#Using GRIDS can increase the performances, so set a as many GRID_MIN and GRID_MAX as the number of CVs with reasonable ranges
+#(i.e an RMSD will range between 0 and 3, while ALPHABETA and DIHCOR will range between 0 and N of dihedrals).
+
+#add here the printing and/or other analyssi
+
+\endplumedfile
+
+\section lugano-6d-conclusions Conclusions
+
+In summary, in this tutorial you should have learned how to use PLUMED to:
+- Analyze trajectories of realistic biological systems using complex CVs
+- Extract conformations that correspond to local free-energy minima
+- Apply block analysis to estimate error in the reconstructed free-energy profiles
+- Calculate ensemble averages of experimental CVs
+- Reweight well-tempered metadynamics simulations
+
+*/
+
+link: @subpage lugano-6d
+
+description: This tutorial propose a more complex case to test your own skill with a more realistic example
diff --git a/user-doc/tutorials/lugano-6c/H-transfer.inp b/user-doc/tutorials/lugano-6c/H-transfer.inp
new file mode 100644
index 0000000000000000000000000000000000000000..9a07ff825e2ef45155ff11b81e1075b2c4fde34f
--- /dev/null
+++ b/user-doc/tutorials/lugano-6c/H-transfer.inp
@@ -0,0 +1,71 @@
+&MOTION
+ &MD
+ ENSEMBLE NVT
+ STEPS 100
+ TIMESTEP 1.0
+ TEMPERATURE 300.0
+ &THERMOSTAT
+ TYPE CSVR
+ &CSVR
+ TIMECON 1.0
+ &END CSVR
+ &END THERMOSTAT
+ &END MD
+# &FREE_ENERGY
+# &METADYN
+# USE_PLUMED .TRUE.
+# PLUMED_INPUT_FILE ./plumed.dat
+# &END METADYN
+# &END FREE_ENERGY
+&END MOTION
+&FORCE_EVAL
+ METHOD Quickstep
+ &DFT
+ BASIS_SET_FILE_NAME BASIS_SET
+ POTENTIAL_FILE_NAME POTENTIAL
+ &MGRID
+ CUTOFF 340
+ REL_CUTOFF 50
+ &END MGRID
+ &SCF
+ EPS_SCF 1.0E-6
+ MAX_SCF 100
+ SCF_GUESS atomic
+ &OT
+ PRECONDITIONER FULL_ALL
+ MINIMIZER DIIS
+ &END OT
+ &END SCF
+ &XC
+ &XC_FUNCTIONAL BLYP
+ &END XC_FUNCTIONAL
+ &END XC
+ &PRINT
+ &E_DENSITY_CUBE
+ &END E_DENSITY_CUBE
+ &END PRINT
+ &END DFT
+ &SUBSYS
+ &CELL
+ ABC 7.83 7.83 7.83
+ &END CELL
+ &TOPOLOGY
+ COORD_FILE_NAME H-transfer.pdb
+ COORD_FILE_FORMAT PDB
+ CONN_FILE_FORMAT OFF
+ &END TOPOLOGY
+ &KIND O
+ BASIS_SET DZVP-GTH-BLYP
+ POTENTIAL GTH-BLYP-q6
+ &END KIND
+ &KIND H
+ BASIS_SET DZVP-GTH-BLYP
+ POTENTIAL GTH-BLYP-q1
+ &END KIND
+ &END SUBSYS
+&END FORCE_EVAL
+&GLOBAL
+ PROJECT water
+ RUN_TYPE MD
+ PRINT_LEVEL LOW
+&END GLOBAL
diff --git a/user-doc/tutorials/lugano-6c/H-transfer.pdb b/user-doc/tutorials/lugano-6c/H-transfer.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..6b7e7cdcbbea3e476c59164e872a33c2c5e81c16
--- /dev/null
+++ b/user-doc/tutorials/lugano-6c/H-transfer.pdb
@@ -0,0 +1,24 @@
+TITLE Great Red Oystrich Makes All Chemists Sane
+REMARK THIS IS A SIMULATION BOX
+CRYST1 7.833 7.833 7.833 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 O X 1 4.581 4.735 5.631 1.00 1.00 O
+ATOM 2 H X 1 5.199 4.170 6.091 1.00 1.00 H
+ATOM 3 H X 1 5.118 5.381 5.164 1.00 1.00 H
+ATOM 4 O X 2 3.653 3.608 3.602 1.00 1.00 O
+ATOM 5 H X 2 3.966 4.159 2.889 1.00 1.00 H
+ATOM 6 H X 2 4.043 3.983 4.401 1.00 1.00 H
+ATOM 7 H X 2 3.000 3.000 3.500 1.00 1.00 H
+ATOM 8 O X 3 1.928 5.497 6.431 1.00 1.00 O
+ATOM 9 H X 3 2.647 5.304 5.854 1.00 1.00 H
+ATOM 10 H X 3 2.328 5.917 7.181 1.00 1.00 H
+ATOM 11 O X 4 0.985 2.453 3.015 1.00 1.00 O
+ATOM 12 H X 4 1.897 2.654 3.256 1.00 1.00 H
+ATOM 13 H X 4 0.599 3.323 2.815 1.00 1.00 H
+ATOM 14 O X 5 5.832 0.673 2.536 1.00 1.00 O
+ATOM 15 H X 5 5.366 1.370 2.061 1.00 1.00 H
+ATOM 16 H X 5 5.324 0.534 3.334 1.00 1.00 H
+ATOM 17 O X 6 6.631 6.362 2.080 1.00 1.00 O
+ATOM 18 H X 6 6.378 5.465 1.850 1.00 1.00 H
+TER
+ENDMDL
diff --git a/user-doc/tutorials/lugano-6d/GB1.mdp b/user-doc/tutorials/lugano-6d/GB1.mdp
new file mode 100644
index 0000000000000000000000000000000000000000..edf690d99005599d4a8156caa328acf2ad8d9469
--- /dev/null
+++ b/user-doc/tutorials/lugano-6d/GB1.mdp
@@ -0,0 +1,352 @@
+;
+; File 'mdout.mdp' was generated
+; By user: jn12 (49673)
+; On host: smogger.rice.edu
+; At date: Sun Jun 21 14:04:41 2015
+;
+
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include =
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define =
+
+; RUN CONTROL PARAMETERS
+integrator = sd
+; Start time and timestep in ps
+tinit = 0
+dt = 0.002
+nsteps = 1000000
+; For exact run continuation or redoing part of a run
+init-step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm_mode = none
+; number of steps for center of mass motion removal
+nstcomm = 50
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 5000
+nstcalcenergy = 100
+nstenergy = 5000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 1000
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps = system
+; Selection of energy groups
+energygrps = system
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = verlet
+; nblist update frequency
+nstlist = 50
+; ns algorithm (simple or grid)
+ns_type = grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1.0
+; long-range cut-off for switched potentials
+rlistlong = -1
+nstcalclr = -1
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1.0
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1.0
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 20
+; Separate tables between energy group pairs
+energygrp-table =
+; Spacing for the PME/PPPM FFT grid
+fourierspacing = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier-nx = 0
+fourier-ny = 0
+fourier-nz = 0
+; EWALD/PME/PPPM parameters
+pme-order = 4
+ewald-rtol = 1e-05
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+
+; IMPLICIT SOLVENT ALGORITHM
+implicit-solvent = No
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb-algorithm = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii = 1
+; Dielectric coefficient of the implicit solvent
+gb-epsilon-solvent = 80
+; Salt concentration in M for Generalized Born models
+gb-saltconc = 0
+; Scaling factors used in the OBC GB model. Default values are OBC(II)
+gb-obc-alpha = 1
+gb-obc-beta = 0.8
+gb-obc-gamma = 4.85
+gb-dielectric-offset = 0.009
+sa-algorithm = Ace-approximation
+; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
+; The value -1 will set default value for Still/HCT/OBC GB-models.
+sa-surface-tension = -1
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps = system
+; Time constant (ps) and reference temperature (K)
+tau_t = 2.0
+ref_t = 115
+; pressure coupling
+Pcoupl = no
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+; Optimization of QM subsystem
+bOPT =
+bTS =
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen_vel = yes
+gen_temp = 115
+gen_seed = -1
+
+; OPTIONS FOR BONDS
+constraints = all-bonds
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 2
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle = 30
+; Convert harmonic bonds to morse potentials
+morse = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+; Pull type: no, umbrella, constraint or constant-force
+pull = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed = no
+disre-fc = 1000
+disre-tau = 0
+; Output frequency for pair distances to energy file
+nstdisreout = 100
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Electric fields
+; Format is number of terms (int) and for all terms an amplitude (real)
+; and a phase angle (real)
+E-x =
+E-xt =
+E-y =
+E-yt =
+E-z =
+E-zt =
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+
+; AdResS parameters
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
diff --git a/user-doc/tutorials/lugano-6d/GB1.tpr b/user-doc/tutorials/lugano-6d/GB1.tpr
new file mode 100644
index 0000000000000000000000000000000000000000..f6ffae4273e45ca5b4c9339a20c9113d741f9ad2
Binary files /dev/null and b/user-doc/tutorials/lugano-6d/GB1.tpr differ
diff --git a/user-doc/tutorials/lugano-6d/GB1_native.pdb b/user-doc/tutorials/lugano-6d/GB1_native.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..a81ad5e1a5fafa0a1a94cf878b19cff5f1a5d2d1
--- /dev/null
+++ b/user-doc/tutorials/lugano-6d/GB1_native.pdb
@@ -0,0 +1,436 @@
+ATOM 1 N MET 1 12.970 18.510 30.950 1.00 1.00
+ATOM 2 CA MET 1 13.940 18.530 29.840 1.00 1.00
+ATOM 3 C MET 1 13.140 18.690 28.520 1.00 1.00
+ATOM 4 O MET 1 12.010 18.220 28.400 1.00 1.00
+ATOM 5 CB MET 1 14.730 17.220 29.880 1.00 1.00
+ATOM 6 CG MET 1 15.740 16.980 28.740 1.00 1.00
+ATOM 7 SD MET 1 17.380 17.020 29.360 1.00 1.00
+ATOM 8 CE MET 1 17.170 16.060 30.820 1.00 1.00
+ATOM 9 N THR 2 13.720 19.410 27.570 1.00 1.00
+ATOM 10 CA THR 2 13.090 19.660 26.280 1.00 1.00
+ATOM 11 C THR 2 13.560 18.630 25.300 1.00 1.00
+ATOM 12 O THR 2 14.760 18.430 25.120 1.00 1.00
+ATOM 13 CB THR 2 13.530 20.980 25.670 1.00 1.00
+ATOM 14 OG1 THR 2 13.310 22.020 26.630 1.00 1.00
+ATOM 15 CG2 THR 2 12.700 21.280 24.410 1.00 1.00
+ATOM 16 N TYR 3 12.570 18.050 24.640 1.00 1.00
+ATOM 17 CA TYR 3 12.730 17.030 23.610 1.00 1.00
+ATOM 18 C TYR 3 12.110 17.640 22.320 1.00 1.00
+ATOM 19 O TYR 3 11.170 18.450 22.360 1.00 1.00
+ATOM 20 CB TYR 3 11.910 15.810 24.040 1.00 1.00
+ATOM 21 CG TYR 3 12.500 15.090 25.200 1.00 1.00
+ATOM 22 CD1 TYR 3 13.560 14.280 25.010 1.00 1.00
+ATOM 23 CD2 TYR 3 12.050 15.320 26.490 1.00 1.00
+ATOM 24 CE1 TYR 3 14.210 13.690 26.060 1.00 1.00
+ATOM 25 CE2 TYR 3 12.660 14.740 27.570 1.00 1.00
+ATOM 26 CZ TYR 3 13.770 13.910 27.320 1.00 1.00
+ATOM 27 OH TYR 3 14.480 13.300 28.340 1.00 1.00
+ATOM 28 N LYS 4 12.630 17.220 21.180 1.00 1.00
+ATOM 29 CA LYS 4 12.180 17.660 19.890 1.00 1.00
+ATOM 30 C LYS 4 11.680 16.470 19.090 1.00 1.00
+ATOM 31 O LYS 4 12.150 15.340 19.240 1.00 1.00
+ATOM 32 CB LYS 4 13.380 18.250 19.100 1.00 1.00
+ATOM 33 CG LYS 4 12.950 19.040 17.860 1.00 1.00
+ATOM 34 CD LYS 4 14.120 19.490 16.980 1.00 1.00
+ATOM 35 CE LYS 4 14.180 21.060 16.750 1.00 1.00
+ATOM 36 NZ LYS 4 12.930 21.820 16.300 1.00 1.00
+ATOM 37 N LEU 5 10.770 16.760 18.160 1.00 1.00
+ATOM 38 CA LEU 5 10.250 15.790 17.220 1.00 1.00
+ATOM 39 C LEU 5 10.360 16.410 15.780 1.00 1.00
+ATOM 40 O LEU 5 9.920 17.540 15.550 1.00 1.00
+ATOM 41 CB LEU 5 8.770 15.470 17.510 1.00 1.00
+ATOM 42 CG LEU 5 8.060 14.610 16.410 1.00 1.00
+ATOM 43 CD1 LEU 5 8.630 13.160 16.370 1.00 1.00
+ATOM 44 CD2 LEU 5 6.580 14.520 16.660 1.00 1.00
+ATOM 45 N ILE 6 10.990 15.690 14.860 1.00 1.00
+ATOM 46 CA ILE 6 11.080 16.100 13.480 1.00 1.00
+ATOM 47 C ILE 6 10.050 15.230 12.750 1.00 1.00
+ATOM 48 O ILE 6 10.070 14.020 12.890 1.00 1.00
+ATOM 49 CB ILE 6 12.480 15.880 12.920 1.00 1.00
+ATOM 50 CG1 ILE 6 13.450 16.790 13.680 1.00 1.00
+ATOM 51 CG2 ILE 6 12.520 16.270 11.430 1.00 1.00
+ATOM 52 CD1 ILE 6 14.840 16.500 13.280 1.00 1.00
+ATOM 53 N LEU 7 9.090 15.850 12.090 1.00 1.00
+ATOM 54 CA LEU 7 8.010 15.160 11.390 1.00 1.00
+ATOM 55 C LEU 7 8.310 15.180 9.900 1.00 1.00
+ATOM 56 O LEU 7 8.580 16.230 9.290 1.00 1.00
+ATOM 57 CB LEU 7 6.690 15.900 11.600 1.00 1.00
+ATOM 58 CG LEU 7 6.150 16.010 13.030 1.00 1.00
+ATOM 59 CD1 LEU 7 5.650 17.410 13.280 1.00 1.00
+ATOM 60 CD2 LEU 7 5.040 14.950 13.250 1.00 1.00
+ATOM 61 N ASN 8 8.380 14.020 9.320 1.00 1.00
+ATOM 62 CA ASN 8 8.630 13.970 7.910 1.00 1.00
+ATOM 63 C ASN 8 7.580 13.040 7.320 1.00 1.00
+ATOM 64 O ASN 8 7.880 11.920 6.940 1.00 1.00
+ATOM 65 CB ASN 8 10.030 13.490 7.680 1.00 1.00
+ATOM 66 CG ASN 8 10.270 13.210 6.230 1.00 1.00
+ATOM 67 OD1 ASN 8 10.130 14.100 5.390 1.00 1.00
+ATOM 68 ND2 ASN 8 10.500 11.960 5.900 1.00 1.00
+ATOM 69 N GLY 9 6.310 13.410 7.480 1.00 1.00
+ATOM 70 CA GLY 9 5.210 12.640 6.970 1.00 1.00
+ATOM 71 C GLY 9 4.910 12.990 5.510 1.00 1.00
+ATOM 72 O GLY 9 5.570 13.840 4.930 1.00 1.00
+ATOM 73 N LYS 10 3.920 12.340 4.910 1.00 1.00
+ATOM 74 CA LYS 10 3.590 12.600 3.500 1.00 1.00
+ATOM 75 C LYS 10 2.910 13.960 3.390 1.00 1.00
+ATOM 76 O LYS 10 3.170 14.710 2.430 1.00 1.00
+ATOM 77 CB LYS 10 2.610 11.570 2.910 1.00 1.00
+ATOM 78 CG LYS 10 2.910 10.140 3.210 1.00 1.00
+ATOM 79 CD LYS 10 1.960 9.180 2.460 1.00 1.00
+ATOM 80 CE LYS 10 0.440 9.230 2.860 1.00 1.00
+ATOM 81 NZ LYS 10 -0.450 10.380 2.320 1.00 1.00
+ATOM 82 N THR 11 2.100 14.250 4.410 1.00 1.00
+ATOM 83 CA THR 11 1.290 15.470 4.540 1.00 1.00
+ATOM 84 C THR 11 1.720 16.510 5.590 1.00 1.00
+ATOM 85 O THR 11 1.570 17.680 5.330 1.00 1.00
+ATOM 86 CB THR 11 -0.180 15.080 4.830 1.00 1.00
+ATOM 87 OG1 THR 11 -0.810 14.770 3.580 1.00 1.00
+ATOM 88 CG2 THR 11 -0.940 16.220 5.480 1.00 1.00
+ATOM 89 N LEU 12 2.200 16.090 6.760 1.00 1.00
+ATOM 90 CA LEU 12 2.620 17.020 7.790 1.00 1.00
+ATOM 91 C LEU 12 4.150 16.950 7.890 1.00 1.00
+ATOM 92 O LEU 12 4.720 15.880 8.030 1.00 1.00
+ATOM 93 CB LEU 12 2.050 16.590 9.110 1.00 1.00
+ATOM 94 CG LEU 12 1.660 17.530 10.260 1.00 1.00
+ATOM 95 CD1 LEU 12 1.510 16.690 11.540 1.00 1.00
+ATOM 96 CD2 LEU 12 2.640 18.670 10.370 1.00 1.00
+ATOM 97 N LYS 13 4.790 18.110 7.810 1.00 1.00
+ATOM 98 CA LYS 13 6.240 18.280 7.900 1.00 1.00
+ATOM 99 C LYS 13 6.600 19.430 8.880 1.00 1.00
+ATOM 100 O LYS 13 5.910 20.420 8.910 1.00 1.00
+ATOM 101 CB LYS 13 6.810 18.600 6.520 1.00 1.00
+ATOM 102 CG LYS 13 6.740 17.390 5.530 1.00 1.00
+ATOM 103 CD LYS 13 7.840 17.510 4.510 1.00 1.00
+ATOM 104 CE LYS 13 8.050 16.220 3.670 1.00 1.00
+ATOM 105 NZ LYS 13 6.800 15.840 3.090 1.00 1.00
+ATOM 106 N GLY 14 7.710 19.310 9.600 1.00 1.00
+ATOM 107 CA GLY 14 8.150 20.350 10.510 1.00 1.00
+ATOM 108 C GLY 14 8.790 19.830 11.800 1.00 1.00
+ATOM 109 O GLY 14 9.300 18.710 11.800 1.00 1.00
+ATOM 110 N GLU 15 8.810 20.640 12.870 1.00 1.00
+ATOM 111 CA GLU 15 9.430 20.300 14.170 1.00 1.00
+ATOM 112 C GLU 15 8.600 20.870 15.250 1.00 1.00
+ATOM 113 O GLU 15 8.080 21.960 15.080 1.00 1.00
+ATOM 114 CB GLU 15 10.720 21.060 14.400 1.00 1.00
+ATOM 115 CG GLU 15 11.690 20.930 13.340 1.00 1.00
+ATOM 116 CD GLU 15 12.920 21.750 13.630 1.00 1.00
+ATOM 117 OE1 GLU 15 12.770 22.950 14.010 1.00 1.00
+ATOM 118 OE2 GLU 15 14.040 21.170 13.560 1.00 1.00
+ATOM 119 N THR 16 8.500 20.130 16.360 1.00 1.00
+ATOM 120 CA THR 16 7.800 20.580 17.590 1.00 1.00
+ATOM 121 C THR 16 8.600 20.130 18.790 1.00 1.00
+ATOM 122 O THR 16 9.450 19.230 18.700 1.00 1.00
+ATOM 123 CB THR 16 6.420 20.020 17.890 1.00 1.00
+ATOM 124 OG1 THR 16 6.250 18.720 17.340 1.00 1.00
+ATOM 125 CG2 THR 16 5.410 20.930 17.470 1.00 1.00
+ATOM 126 N THR 17 8.320 20.730 19.930 1.00 1.00
+ATOM 127 CA THR 17 9.060 20.310 21.100 1.00 1.00
+ATOM 128 C THR 17 8.070 20.070 22.200 1.00 1.00
+ATOM 129 O THR 17 6.870 20.260 22.040 1.00 1.00
+ATOM 130 CB THR 17 10.080 21.390 21.510 1.00 1.00
+ATOM 131 OG1 THR 17 9.370 22.540 21.930 1.00 1.00
+ATOM 132 CG2 THR 17 10.980 21.780 20.360 1.00 1.00
+ATOM 133 N THR 18 8.560 19.530 23.290 1.00 1.00
+ATOM 134 CA THR 18 7.740 19.310 24.470 1.00 1.00
+ATOM 135 C THR 18 8.690 19.190 25.670 1.00 1.00
+ATOM 136 O THR 18 9.880 19.020 25.510 1.00 1.00
+ATOM 137 CB THR 18 6.810 18.020 24.370 1.00 1.00
+ATOM 138 OG1 THR 18 5.840 18.120 25.410 1.00 1.00
+ATOM 139 CG2 THR 18 7.600 16.670 24.590 1.00 1.00
+ATOM 140 N GLU 19 8.170 19.470 26.850 1.00 1.00
+ATOM 141 CA GLU 19 8.910 19.330 28.090 1.00 1.00
+ATOM 142 C GLU 19 8.420 18.020 28.650 1.00 1.00
+ATOM 143 O GLU 19 7.220 17.770 28.690 1.00 1.00
+ATOM 144 CB GLU 19 8.480 20.360 29.130 1.00 1.00
+ATOM 145 CG GLU 19 8.490 21.750 28.660 1.00 1.00
+ATOM 146 CD GLU 19 9.860 22.240 28.310 1.00 1.00
+ATOM 147 OE1 GLU 19 10.750 22.040 29.160 1.00 1.00
+ATOM 148 OE2 GLU 19 10.050 22.860 27.210 1.00 1.00
+ATOM 149 N ALA 20 9.350 17.210 29.140 1.00 1.00
+ATOM 150 CA ALA 20 8.980 15.930 29.750 1.00 1.00
+ATOM 151 C ALA 20 10.070 15.610 30.760 1.00 1.00
+ATOM 152 O ALA 20 11.190 16.120 30.690 1.00 1.00
+ATOM 153 CB ALA 20 8.860 14.820 28.710 1.00 1.00
+ATOM 154 N VAL 21 9.700 14.800 31.740 1.00 1.00
+ATOM 155 CA VAL 21 10.640 14.410 32.790 1.00 1.00
+ATOM 156 C VAL 21 11.690 13.490 32.190 1.00 1.00
+ATOM 157 O VAL 21 12.870 13.630 32.490 1.00 1.00
+ATOM 158 CB VAL 21 9.880 13.680 33.930 1.00 1.00
+ATOM 159 CG1 VAL 21 8.550 14.520 34.310 1.00 1.00
+ATOM 160 CG2 VAL 21 9.490 12.250 33.490 1.00 1.00
+ATOM 161 N ASP 22 11.280 12.590 31.280 1.00 1.00
+ATOM 162 CA ASP 22 12.220 11.680 30.660 1.00 1.00
+ATOM 163 C ASP 22 11.860 11.330 29.220 1.00 1.00
+ATOM 164 O ASP 22 10.820 11.700 28.730 1.00 1.00
+ATOM 165 CB ASP 22 12.370 10.400 31.500 1.00 1.00
+ATOM 166 CG ASP 22 11.140 9.510 31.520 1.00 1.00
+ATOM 167 OD1 ASP 22 10.030 9.930 31.190 1.00 1.00
+ATOM 168 OD2 ASP 22 11.280 8.350 31.890 1.00 1.00
+ATOM 169 N ALA 23 12.670 10.490 28.600 1.00 1.00
+ATOM 170 CA ALA 23 12.450 10.120 27.230 1.00 1.00
+ATOM 171 C ALA 23 11.260 9.260 26.940 1.00 1.00
+ATOM 172 O ALA 23 10.660 9.460 25.920 1.00 1.00
+ATOM 173 CB ALA 23 13.710 9.530 26.600 1.00 1.00
+ATOM 174 N ALA 24 10.850 8.380 27.840 1.00 1.00
+ATOM 175 CA ALA 24 9.680 7.540 27.580 1.00 1.00
+ATOM 176 C ALA 24 8.400 8.350 27.690 1.00 1.00
+ATOM 177 O ALA 24 7.360 8.040 27.080 1.00 1.00
+ATOM 178 CB ALA 24 9.640 6.390 28.600 1.00 1.00
+ATOM 179 N THR 25 8.440 9.400 28.480 1.00 1.00
+ATOM 180 CA THR 25 7.250 10.210 28.620 1.00 1.00
+ATOM 181 C THR 25 7.090 11.060 27.380 1.00 1.00
+ATOM 182 O THR 25 5.960 11.260 26.900 1.00 1.00
+ATOM 183 CB THR 25 7.320 11.090 29.870 1.00 1.00
+ATOM 184 OG1 THR 25 7.510 10.240 31.010 1.00 1.00
+ATOM 185 CG2 THR 25 6.030 11.790 30.090 1.00 1.00
+ATOM 186 N ALA 26 8.200 11.600 26.880 1.00 1.00
+ATOM 187 CA ALA 26 8.150 12.440 25.680 1.00 1.00
+ATOM 188 C ALA 26 7.710 11.630 24.420 1.00 1.00
+ATOM 189 O ALA 26 6.940 12.110 23.580 1.00 1.00
+ATOM 190 CB ALA 26 9.460 13.160 25.470 1.00 1.00
+ATOM 191 N GLU 27 8.150 10.380 24.340 1.00 1.00
+ATOM 192 CA GLU 27 7.820 9.450 23.250 1.00 1.00
+ATOM 193 C GLU 27 6.310 9.170 23.270 1.00 1.00
+ATOM 194 O GLU 27 5.670 9.070 22.250 1.00 1.00
+ATOM 195 CB GLU 27 8.570 8.140 23.440 1.00 1.00
+ATOM 196 CG GLU 27 8.520 7.310 22.200 1.00 1.00
+ATOM 197 CD GLU 27 8.630 5.840 22.500 1.00 1.00
+ATOM 198 OE1 GLU 27 9.620 5.400 23.080 1.00 1.00
+ATOM 199 OE2 GLU 27 7.740 5.090 22.130 1.00 1.00
+ATOM 200 N LYS 28 5.740 9.140 24.460 1.00 1.00
+ATOM 201 CA LYS 28 4.310 8.920 24.680 1.00 1.00
+ATOM 202 C LYS 28 3.510 10.060 24.080 1.00 1.00
+ATOM 203 O LYS 28 2.560 9.840 23.320 1.00 1.00
+ATOM 204 CB LYS 28 4.030 8.930 26.200 1.00 1.00
+ATOM 205 CG LYS 28 3.240 7.790 26.720 1.00 1.00
+ATOM 206 CD LYS 28 3.370 7.850 28.260 1.00 1.00
+ATOM 207 CE LYS 28 4.840 7.590 28.790 1.00 1.00
+ATOM 208 NZ LYS 28 5.000 7.900 30.270 1.00 1.00
+ATOM 209 N VAL 29 3.810 11.270 24.510 1.00 1.00
+ATOM 210 CA VAL 29 3.070 12.380 23.980 1.00 1.00
+ATOM 211 C VAL 29 3.320 12.570 22.460 1.00 1.00
+ATOM 212 O VAL 29 2.400 12.980 21.750 1.00 1.00
+ATOM 213 CB VAL 29 3.280 13.700 24.770 1.00 1.00
+ATOM 214 CG1 VAL 29 2.660 14.910 24.040 1.00 1.00
+ATOM 215 CG2 VAL 29 2.730 13.590 26.070 1.00 1.00
+ATOM 216 N PHE 30 4.550 12.320 21.970 1.00 1.00
+ATOM 217 CA PHE 30 4.840 12.490 20.530 1.00 1.00
+ATOM 218 C PHE 30 4.080 11.470 19.690 1.00 1.00
+ATOM 219 O PHE 30 3.480 11.800 18.680 1.00 1.00
+ATOM 220 CB PHE 30 6.350 12.500 20.260 1.00 1.00
+ATOM 221 CG PHE 30 7.040 13.800 20.670 1.00 1.00
+ATOM 222 CD1 PHE 30 6.400 15.040 20.580 1.00 1.00
+ATOM 223 CD2 PHE 30 8.380 13.820 21.060 1.00 1.00
+ATOM 224 CE1 PHE 30 7.110 16.240 20.870 1.00 1.00
+ATOM 225 CE2 PHE 30 9.030 15.020 21.330 1.00 1.00
+ATOM 226 CZ PHE 30 8.420 16.200 21.240 1.00 1.00
+ATOM 227 N LYS 31 4.010 10.240 20.160 1.00 1.00
+ATOM 228 CA LYS 31 3.250 9.230 19.460 1.00 1.00
+ATOM 229 C LYS 31 1.750 9.610 19.370 1.00 1.00
+ATOM 230 O LYS 31 1.180 9.470 18.300 1.00 1.00
+ATOM 231 CB LYS 31 3.450 7.870 20.070 1.00 1.00
+ATOM 232 CG LYS 31 4.870 7.470 19.980 1.00 1.00
+ATOM 233 CD LYS 31 5.090 6.410 18.940 1.00 1.00
+ATOM 234 CE LYS 31 6.190 5.400 19.360 1.00 1.00
+ATOM 235 NZ LYS 31 5.820 4.560 20.560 1.00 1.00
+ATOM 236 N GLN 32 1.140 10.080 20.460 1.00 1.00
+ATOM 237 CA GLN 32 -0.280 10.490 20.450 1.00 1.00
+ATOM 238 C GLN 32 -0.470 11.630 19.520 1.00 1.00
+ATOM 239 O GLN 32 -1.400 11.640 18.770 1.00 1.00
+ATOM 240 CB GLN 32 -0.740 10.940 21.830 1.00 1.00
+ATOM 241 CG GLN 32 -0.880 9.780 22.750 1.00 1.00
+ATOM 242 CD GLN 32 -1.800 10.070 23.880 1.00 1.00
+ATOM 243 OE1 GLN 32 -1.550 10.970 24.700 1.00 1.00
+ATOM 244 NE2 GLN 32 -2.930 9.330 23.930 1.00 1.00
+ATOM 245 N TYR 33 0.440 12.580 19.530 1.00 1.00
+ATOM 246 CA TYR 33 0.340 13.740 18.650 1.00 1.00
+ATOM 247 C TYR 33 0.430 13.360 17.170 1.00 1.00
+ATOM 248 O TYR 33 -0.270 13.930 16.320 1.00 1.00
+ATOM 249 CB TYR 33 1.430 14.740 19.000 1.00 1.00
+ATOM 250 CG TYR 33 1.580 15.840 17.980 1.00 1.00
+ATOM 251 CD1 TYR 33 0.660 16.890 17.890 1.00 1.00
+ATOM 252 CD2 TYR 33 2.680 15.860 17.160 1.00 1.00
+ATOM 253 CE1 TYR 33 0.860 17.980 16.970 1.00 1.00
+ATOM 254 CE2 TYR 33 2.910 16.920 16.250 1.00 1.00
+ATOM 255 CZ TYR 33 2.010 17.970 16.170 1.00 1.00
+ATOM 256 OH TYR 33 2.360 19.020 15.350 1.00 1.00
+ATOM 257 N ALA 34 1.320 12.410 16.860 1.00 1.00
+ATOM 258 CA ALA 34 1.530 11.950 15.490 1.00 1.00
+ATOM 259 C ALA 34 0.290 11.210 15.040 1.00 1.00
+ATOM 260 O ALA 34 -0.280 11.460 13.990 1.00 1.00
+ATOM 261 CB ALA 34 2.760 11.040 15.440 1.00 1.00
+ATOM 262 N ASN 35 -0.210 10.370 15.910 1.00 1.00
+ATOM 263 CA ASN 35 -1.400 9.620 15.650 1.00 1.00
+ATOM 264 C ASN 35 -2.660 10.510 15.540 1.00 1.00
+ATOM 265 O ASN 35 -3.550 10.220 14.780 1.00 1.00
+ATOM 266 CB ASN 35 -1.550 8.570 16.730 1.00 1.00
+ATOM 267 CG ASN 35 -2.660 7.610 16.460 1.00 1.00
+ATOM 268 OD1 ASN 35 -2.570 6.780 15.560 1.00 1.00
+ATOM 269 ND2 ASN 35 -3.740 7.730 17.220 1.00 1.00
+ATOM 270 N ASP 36 -2.730 11.610 16.250 1.00 1.00
+ATOM 271 CA ASP 36 -3.920 12.440 16.160 1.00 1.00
+ATOM 272 C ASP 36 -3.920 13.160 14.810 1.00 1.00
+ATOM 273 O ASP 36 -4.940 13.680 14.350 1.00 1.00
+ATOM 274 CB ASP 36 -3.870 13.530 17.220 1.00 1.00
+ATOM 275 CG ASP 36 -4.280 13.070 18.620 1.00 1.00
+ATOM 276 OD1 ASP 36 -4.860 11.990 18.830 1.00 1.00
+ATOM 277 OD2 ASP 36 -4.010 13.840 19.540 1.00 1.00
+ATOM 278 N ASN 37 -2.720 13.370 14.280 1.00 1.00
+ATOM 279 CA ASN 37 -2.540 14.060 13.010 1.00 1.00
+ATOM 280 C ASN 37 -2.340 13.090 11.830 1.00 1.00
+ATOM 281 O ASN 37 -1.860 13.500 10.790 1.00 1.00
+ATOM 282 CB ASN 37 -1.420 15.080 13.110 1.00 1.00
+ATOM 283 CG ASN 37 -1.810 16.280 13.980 1.00 1.00
+ATOM 284 OD1 ASN 37 -2.360 17.310 13.510 1.00 1.00
+ATOM 285 ND2 ASN 37 -1.530 16.160 15.270 1.00 1.00
+ATOM 286 N GLY 38 -2.760 11.830 12.030 1.00 1.00
+ATOM 287 CA GLY 38 -2.680 10.790 11.030 1.00 1.00
+ATOM 288 C GLY 38 -1.320 10.340 10.490 1.00 1.00
+ATOM 289 O GLY 38 -1.290 9.680 9.480 1.00 1.00
+ATOM 290 N VAL 39 -0.220 10.680 11.160 1.00 1.00
+ATOM 291 CA VAL 39 1.110 10.310 10.730 1.00 1.00
+ATOM 292 C VAL 39 1.380 8.920 11.250 1.00 1.00
+ATOM 293 O VAL 39 1.130 8.620 12.410 1.00 1.00
+ATOM 294 CB VAL 39 2.100 11.330 11.240 1.00 1.00
+ATOM 295 CG1 VAL 39 3.520 10.930 10.970 1.00 1.00
+ATOM 296 CG2 VAL 39 1.850 12.590 10.550 1.00 1.00
+ATOM 297 N ASP 40 1.910 8.060 10.380 1.00 1.00
+ATOM 298 CA ASP 40 2.170 6.700 10.740 1.00 1.00
+ATOM 299 C ASP 40 3.470 6.300 10.070 1.00 1.00
+ATOM 300 O ASP 40 3.470 5.950 8.900 1.00 1.00
+ATOM 301 CB ASP 40 0.970 5.960 10.190 1.00 1.00
+ATOM 302 CG ASP 40 1.060 4.460 10.340 1.00 1.00
+ATOM 303 OD1 ASP 40 1.680 3.920 11.320 1.00 1.00
+ATOM 304 OD2 ASP 40 0.480 3.810 9.430 1.00 1.00
+ATOM 305 N GLY 41 4.600 6.410 10.740 1.00 1.00
+ATOM 306 CA GLY 41 5.830 6.030 10.070 1.00 1.00
+ATOM 307 C GLY 41 6.850 5.280 10.920 1.00 1.00
+ATOM 308 O GLY 41 6.430 4.620 11.880 1.00 1.00
+ATOM 309 N GLU 42 8.140 5.300 10.540 1.00 1.00
+ATOM 310 CA GLU 42 9.220 4.650 11.310 1.00 1.00
+ATOM 311 C GLU 42 9.740 5.730 12.210 1.00 1.00
+ATOM 312 O GLU 42 9.870 6.860 11.800 1.00 1.00
+ATOM 313 CB GLU 42 10.370 4.280 10.420 1.00 1.00
+ATOM 314 CG GLU 42 10.010 3.530 9.210 1.00 1.00
+ATOM 315 CD GLU 42 9.420 2.120 9.480 1.00 1.00
+ATOM 316 OE1 GLU 42 8.920 1.830 10.640 1.00 1.00
+ATOM 317 OE2 GLU 42 9.410 1.310 8.470 1.00 1.00
+ATOM 318 N TRP 43 10.160 5.340 13.390 1.00 1.00
+ATOM 319 CA TRP 43 10.630 6.260 14.430 1.00 1.00
+ATOM 320 C TRP 43 12.040 6.050 14.840 1.00 1.00
+ATOM 321 O TRP 43 12.490 4.910 14.890 1.00 1.00
+ATOM 322 CB TRP 43 9.780 5.990 15.670 1.00 1.00
+ATOM 323 CG TRP 43 8.350 6.470 15.590 1.00 1.00
+ATOM 324 CD1 TRP 43 7.280 5.880 14.940 1.00 1.00
+ATOM 325 CD2 TRP 43 7.850 7.690 16.150 1.00 1.00
+ATOM 326 NE1 TRP 43 6.160 6.670 15.070 1.00 1.00
+ATOM 327 CE2 TRP 43 6.490 7.780 15.790 1.00 1.00
+ATOM 328 CE3 TRP 43 8.440 8.710 16.910 1.00 1.00
+ATOM 329 CZ2 TRP 43 5.700 8.850 16.150 1.00 1.00
+ATOM 330 CZ3 TRP 43 7.660 9.780 17.270 1.00 1.00
+ATOM 331 CH2 TRP 43 6.280 9.840 16.880 1.00 1.00
+ATOM 332 N THR 44 12.770 7.130 15.130 1.00 1.00
+ATOM 333 CA THR 44 14.120 6.980 15.680 1.00 1.00
+ATOM 334 C THR 44 14.240 7.950 16.840 1.00 1.00
+ATOM 335 O THR 44 13.440 8.900 16.920 1.00 1.00
+ATOM 336 CB THR 44 15.240 7.320 14.750 1.00 1.00
+ATOM 337 OG1 THR 44 15.260 8.720 14.530 1.00 1.00
+ATOM 338 CG2 THR 44 15.110 6.600 13.430 1.00 1.00
+ATOM 339 N TYR 45 15.140 7.650 17.790 1.00 1.00
+ATOM 340 CA TYR 45 15.400 8.490 18.950 1.00 1.00
+ATOM 341 C TYR 45 16.900 8.530 19.190 1.00 1.00
+ATOM 342 O TYR 45 17.580 7.510 19.050 1.00 1.00
+ATOM 343 CB TYR 45 14.680 8.030 20.190 1.00 1.00
+ATOM 344 CG TYR 45 15.070 8.870 21.420 1.00 1.00
+ATOM 345 CD1 TYR 45 14.750 10.240 21.500 1.00 1.00
+ATOM 346 CD2 TYR 45 15.810 8.310 22.470 1.00 1.00
+ATOM 347 CE1 TYR 45 15.160 11.010 22.540 1.00 1.00
+ATOM 348 CE2 TYR 45 16.220 9.100 23.540 1.00 1.00
+ATOM 349 CZ TYR 45 15.890 10.450 23.560 1.00 1.00
+ATOM 350 OH TYR 45 16.280 11.230 24.640 1.00 1.00
+ATOM 351 N ASP 46 17.400 9.760 19.290 1.00 1.00
+ATOM 352 CA ASP 46 18.800 10.070 19.520 1.00 1.00
+ATOM 353 C ASP 46 18.890 10.830 20.860 1.00 1.00
+ATOM 354 O ASP 46 18.580 12.020 20.950 1.00 1.00
+ATOM 355 CB ASP 46 19.330 10.950 18.410 1.00 1.00
+ATOM 356 CG ASP 46 20.810 11.200 18.530 1.00 1.00
+ATOM 357 OD1 ASP 46 21.380 10.990 19.610 1.00 1.00
+ATOM 358 OD2 ASP 46 21.440 11.620 17.520 1.00 1.00
+ATOM 359 N ASP 47 19.450 10.160 21.840 1.00 1.00
+ATOM 360 CA ASP 47 19.600 10.680 23.190 1.00 1.00
+ATOM 361 C ASP 47 20.680 11.710 23.370 1.00 1.00
+ATOM 362 O ASP 47 20.740 12.350 24.430 1.00 1.00
+ATOM 363 CB ASP 47 19.810 9.530 24.140 1.00 1.00
+ATOM 364 CG ASP 47 19.660 9.940 25.570 1.00 1.00
+ATOM 365 OD1 ASP 47 18.720 10.720 25.890 1.00 1.00
+ATOM 366 OD2 ASP 47 20.480 9.450 26.360 1.00 1.00
+ATOM 367 N ALA 48 21.530 11.870 22.360 1.00 1.00
+ATOM 368 CA ALA 48 22.580 12.860 22.350 1.00 1.00
+ATOM 369 C ALA 48 22.060 14.260 21.930 1.00 1.00
+ATOM 370 O ALA 48 22.760 15.270 22.080 1.00 1.00
+ATOM 371 CB ALA 48 23.680 12.430 21.380 1.00 1.00
+ATOM 372 N THR 49 20.880 14.320 21.330 1.00 1.00
+ATOM 373 CA THR 49 20.340 15.600 20.940 1.00 1.00
+ATOM 374 C THR 49 18.910 15.670 21.390 1.00 1.00
+ATOM 375 O THR 49 18.230 16.620 21.100 1.00 1.00
+ATOM 376 CB THR 49 20.400 15.770 19.440 1.00 1.00
+ATOM 377 OG1 THR 49 19.680 14.710 18.800 1.00 1.00
+ATOM 378 CG2 THR 49 21.820 15.730 18.970 1.00 1.00
+ATOM 379 N LYS 50 18.420 14.600 22.020 1.00 1.00
+ATOM 380 CA LYS 50 17.090 14.520 22.580 1.00 1.00
+ATOM 381 C LYS 50 16.050 14.760 21.510 1.00 1.00
+ATOM 382 O LYS 50 15.030 15.430 21.750 1.00 1.00
+ATOM 383 CB LYS 50 16.940 15.530 23.740 1.00 1.00
+ATOM 384 CG LYS 50 17.310 14.980 25.200 1.00 1.00
+ATOM 385 CD LYS 50 18.770 14.870 25.400 1.00 1.00
+ATOM 386 CE LYS 50 19.150 13.950 26.530 1.00 1.00
+ATOM 387 NZ LYS 50 20.640 13.870 26.460 1.00 1.00
+ATOM 388 N THR 51 16.290 14.170 20.360 1.00 1.00
+ATOM 389 CA THR 51 15.430 14.340 19.200 1.00 1.00
+ATOM 390 C THR 51 14.830 13.030 18.690 1.00 1.00
+ATOM 391 O THR 51 15.510 12.000 18.640 1.00 1.00
+ATOM 392 CB THR 51 16.230 14.970 18.110 1.00 1.00
+ATOM 393 OG1 THR 51 16.670 16.250 18.570 1.00 1.00
+ATOM 394 CG2 THR 51 15.420 15.120 16.870 1.00 1.00
+ATOM 395 N PHE 52 13.520 13.060 18.490 1.00 1.00
+ATOM 396 CA PHE 52 12.770 11.940 17.920 1.00 1.00
+ATOM 397 C PHE 52 12.510 12.280 16.460 1.00 1.00
+ATOM 398 O PHE 52 12.490 13.470 16.050 1.00 1.00
+ATOM 399 CB PHE 52 11.390 11.790 18.550 1.00 1.00
+ATOM 400 CG PHE 52 11.410 11.330 19.930 1.00 1.00
+ATOM 401 CD1 PHE 52 11.590 12.220 20.990 1.00 1.00
+ATOM 402 CD2 PHE 52 11.230 9.980 20.230 1.00 1.00
+ATOM 403 CE1 PHE 52 11.580 11.770 22.320 1.00 1.00
+ATOM 404 CE2 PHE 52 11.230 9.540 21.610 1.00 1.00
+ATOM 405 CZ PHE 52 11.410 10.440 22.600 1.00 1.00
+ATOM 406 N THR 53 12.390 11.250 15.640 1.00 1.00
+ATOM 407 CA THR 53 11.970 11.550 14.290 1.00 1.00
+ATOM 408 C THR 53 10.950 10.510 13.810 1.00 1.00
+ATOM 409 O THR 53 11.060 9.340 14.170 1.00 1.00
+ATOM 410 CB THR 53 13.120 11.620 13.260 1.00 1.00
+ATOM 411 OG1 THR 53 13.530 10.270 12.930 1.00 1.00
+ATOM 412 CG2 THR 53 14.270 12.420 13.780 1.00 1.00
+ATOM 413 N VAL 54 9.950 10.940 13.040 1.00 1.00
+ATOM 414 CA VAL 54 8.970 10.040 12.480 1.00 1.00
+ATOM 415 C VAL 54 8.950 10.270 10.940 1.00 1.00
+ATOM 416 O VAL 54 8.840 11.410 10.480 1.00 1.00
+ATOM 417 CB VAL 54 7.540 10.150 13.120 1.00 1.00
+ATOM 418 CG1 VAL 54 6.960 11.600 13.020 1.00 1.00
+ATOM 419 CG2 VAL 54 6.590 9.140 12.420 1.00 1.00
+ATOM 420 N THR 55 9.120 9.210 10.180 1.00 1.00
+ATOM 421 CA THR 55 9.150 9.340 8.720 1.00 1.00
+ATOM 422 C THR 55 8.100 8.480 8.020 1.00 1.00
+ATOM 423 O THR 55 8.030 7.300 8.320 1.00 1.00
+ATOM 424 CB THR 55 10.520 8.930 8.220 1.00 1.00
+ATOM 425 OG1 THR 55 11.470 9.850 8.730 1.00 1.00
+ATOM 426 CG2 THR 55 10.600 8.950 6.680 1.00 1.00
+ATOM 427 N GLUT 56 7.250 9.040 7.180 1.00 1.00
+ATOM 428 CA GLUT 56 6.280 8.180 6.480 1.00 1.00
+ATOM 429 C GLUT 56 6.780 7.740 5.080 1.00 1.00
+ATOM 430 O GLUT 56 7.520 8.520 4.400 1.00 1.00
+ATOM 431 CB GLUT 56 4.960 8.860 6.310 1.00 1.00
+ATOM 432 CG GLUT 56 4.090 8.870 7.510 1.00 1.00
+ATOM 433 CD GLUT 56 2.700 9.420 7.200 1.00 1.00
+ATOM 434 OE1 GLUT 56 2.540 10.440 6.500 1.00 1.00
+ATOM 435 OE2 GLUT 56 1.740 8.790 7.640 1.00 1.00
+ATOM 436 OXT GLUT 56 6.410 6.620 4.670 1.00 1.00
diff --git a/user-doc/tutorials/lugano-6d/GB1_smog.top b/user-doc/tutorials/lugano-6d/GB1_smog.top
new file mode 100644
index 0000000000000000000000000000000000000000..92cc9f5d2da009c0dd847668dc13021a965cdc84
--- /dev/null
+++ b/user-doc/tutorials/lugano-6d/GB1_smog.top
@@ -0,0 +1,3820 @@
+; Structure-based "SMOG" model for use with GROMACS, or NAMD
+; Generated by the SMOG tool version 2.1beta
+; Called with PDB: 1pgb.pdb
+; Created using templates found in directory: /Users/carlo/Codes/Smog2/SBM_AA
+; Your input arguments were: -i 1pgb.pdb -AA
+
+[ defaults ]
+; nbfunc comb-rule gen-pairs
+ 1 1 no
+
+ [ atomtypes ]
+; name mass charge ptype c6 c12
+ NB_1 1.000 0.000 A 0.00000e+00 5.96046e-09
+
+[ moleculetype ]
+; name nrexcl
+ Macromolecule 3
+
+[ atoms ]
+;nr type resnr residue atom cgnr
+ 1 NB_1 1 MET N 1
+ 2 NB_1 1 MET CA 2
+ 3 NB_1 1 MET C 3
+ 4 NB_1 1 MET O 4
+ 5 NB_1 1 MET CB 5
+ 6 NB_1 1 MET CG 6
+ 7 NB_1 1 MET SD 7
+ 8 NB_1 1 MET CE 8
+ 9 NB_1 2 THR N 9
+ 10 NB_1 2 THR CA 10
+ 11 NB_1 2 THR C 11
+ 12 NB_1 2 THR O 12
+ 13 NB_1 2 THR CB 13
+ 14 NB_1 2 THR OG1 14
+ 15 NB_1 2 THR CG2 15
+ 16 NB_1 3 TYR N 16
+ 17 NB_1 3 TYR CA 17
+ 18 NB_1 3 TYR C 18
+ 19 NB_1 3 TYR O 19
+ 20 NB_1 3 TYR CB 20
+ 21 NB_1 3 TYR CG 21
+ 22 NB_1 3 TYR CD1 22
+ 23 NB_1 3 TYR CD2 23
+ 24 NB_1 3 TYR CE1 24
+ 25 NB_1 3 TYR CE2 25
+ 26 NB_1 3 TYR CZ 26
+ 27 NB_1 3 TYR OH 27
+ 28 NB_1 4 LYS N 28
+ 29 NB_1 4 LYS CA 29
+ 30 NB_1 4 LYS C 30
+ 31 NB_1 4 LYS O 31
+ 32 NB_1 4 LYS CB 32
+ 33 NB_1 4 LYS CG 33
+ 34 NB_1 4 LYS CD 34
+ 35 NB_1 4 LYS CE 35
+ 36 NB_1 4 LYS NZ 36
+ 37 NB_1 5 LEU N 37
+ 38 NB_1 5 LEU CA 38
+ 39 NB_1 5 LEU C 39
+ 40 NB_1 5 LEU O 40
+ 41 NB_1 5 LEU CB 41
+ 42 NB_1 5 LEU CG 42
+ 43 NB_1 5 LEU CD1 43
+ 44 NB_1 5 LEU CD2 44
+ 45 NB_1 6 ILE N 45
+ 46 NB_1 6 ILE CA 46
+ 47 NB_1 6 ILE C 47
+ 48 NB_1 6 ILE O 48
+ 49 NB_1 6 ILE CB 49
+ 50 NB_1 6 ILE CG1 50
+ 51 NB_1 6 ILE CG2 51
+ 52 NB_1 6 ILE CD1 52
+ 53 NB_1 7 LEU N 53
+ 54 NB_1 7 LEU CA 54
+ 55 NB_1 7 LEU C 55
+ 56 NB_1 7 LEU O 56
+ 57 NB_1 7 LEU CB 57
+ 58 NB_1 7 LEU CG 58
+ 59 NB_1 7 LEU CD1 59
+ 60 NB_1 7 LEU CD2 60
+ 61 NB_1 8 ASN N 61
+ 62 NB_1 8 ASN CA 62
+ 63 NB_1 8 ASN C 63
+ 64 NB_1 8 ASN O 64
+ 65 NB_1 8 ASN CB 65
+ 66 NB_1 8 ASN CG 66
+ 67 NB_1 8 ASN OD1 67
+ 68 NB_1 8 ASN ND2 68
+ 69 NB_1 9 GLY N 69
+ 70 NB_1 9 GLY CA 70
+ 71 NB_1 9 GLY C 71
+ 72 NB_1 9 GLY O 72
+ 73 NB_1 10 LYS N 73
+ 74 NB_1 10 LYS CA 74
+ 75 NB_1 10 LYS C 75
+ 76 NB_1 10 LYS O 76
+ 77 NB_1 10 LYS CB 77
+ 78 NB_1 10 LYS CG 78
+ 79 NB_1 10 LYS CD 79
+ 80 NB_1 10 LYS CE 80
+ 81 NB_1 10 LYS NZ 81
+ 82 NB_1 11 THR N 82
+ 83 NB_1 11 THR CA 83
+ 84 NB_1 11 THR C 84
+ 85 NB_1 11 THR O 85
+ 86 NB_1 11 THR CB 86
+ 87 NB_1 11 THR OG1 87
+ 88 NB_1 11 THR CG2 88
+ 89 NB_1 12 LEU N 89
+ 90 NB_1 12 LEU CA 90
+ 91 NB_1 12 LEU C 91
+ 92 NB_1 12 LEU O 92
+ 93 NB_1 12 LEU CB 93
+ 94 NB_1 12 LEU CG 94
+ 95 NB_1 12 LEU CD1 95
+ 96 NB_1 12 LEU CD2 96
+ 97 NB_1 13 LYS N 97
+ 98 NB_1 13 LYS CA 98
+ 99 NB_1 13 LYS C 99
+ 100 NB_1 13 LYS O 100
+ 101 NB_1 13 LYS CB 101
+ 102 NB_1 13 LYS CG 102
+ 103 NB_1 13 LYS CD 103
+ 104 NB_1 13 LYS CE 104
+ 105 NB_1 13 LYS NZ 105
+ 106 NB_1 14 GLY N 106
+ 107 NB_1 14 GLY CA 107
+ 108 NB_1 14 GLY C 108
+ 109 NB_1 14 GLY O 109
+ 110 NB_1 15 GLU N 110
+ 111 NB_1 15 GLU CA 111
+ 112 NB_1 15 GLU C 112
+ 113 NB_1 15 GLU O 113
+ 114 NB_1 15 GLU CB 114
+ 115 NB_1 15 GLU CG 115
+ 116 NB_1 15 GLU CD 116
+ 117 NB_1 15 GLU OE1 117
+ 118 NB_1 15 GLU OE2 118
+ 119 NB_1 16 THR N 119
+ 120 NB_1 16 THR CA 120
+ 121 NB_1 16 THR C 121
+ 122 NB_1 16 THR O 122
+ 123 NB_1 16 THR CB 123
+ 124 NB_1 16 THR OG1 124
+ 125 NB_1 16 THR CG2 125
+ 126 NB_1 17 THR N 126
+ 127 NB_1 17 THR CA 127
+ 128 NB_1 17 THR C 128
+ 129 NB_1 17 THR O 129
+ 130 NB_1 17 THR CB 130
+ 131 NB_1 17 THR OG1 131
+ 132 NB_1 17 THR CG2 132
+ 133 NB_1 18 THR N 133
+ 134 NB_1 18 THR CA 134
+ 135 NB_1 18 THR C 135
+ 136 NB_1 18 THR O 136
+ 137 NB_1 18 THR CB 137
+ 138 NB_1 18 THR OG1 138
+ 139 NB_1 18 THR CG2 139
+ 140 NB_1 19 GLU N 140
+ 141 NB_1 19 GLU CA 141
+ 142 NB_1 19 GLU C 142
+ 143 NB_1 19 GLU O 143
+ 144 NB_1 19 GLU CB 144
+ 145 NB_1 19 GLU CG 145
+ 146 NB_1 19 GLU CD 146
+ 147 NB_1 19 GLU OE1 147
+ 148 NB_1 19 GLU OE2 148
+ 149 NB_1 20 ALA N 149
+ 150 NB_1 20 ALA CA 150
+ 151 NB_1 20 ALA C 151
+ 152 NB_1 20 ALA O 152
+ 153 NB_1 20 ALA CB 153
+ 154 NB_1 21 VAL N 154
+ 155 NB_1 21 VAL CA 155
+ 156 NB_1 21 VAL C 156
+ 157 NB_1 21 VAL O 157
+ 158 NB_1 21 VAL CB 158
+ 159 NB_1 21 VAL CG1 159
+ 160 NB_1 21 VAL CG2 160
+ 161 NB_1 22 ASP N 161
+ 162 NB_1 22 ASP CA 162
+ 163 NB_1 22 ASP C 163
+ 164 NB_1 22 ASP O 164
+ 165 NB_1 22 ASP CB 165
+ 166 NB_1 22 ASP CG 166
+ 167 NB_1 22 ASP OD1 167
+ 168 NB_1 22 ASP OD2 168
+ 169 NB_1 23 ALA N 169
+ 170 NB_1 23 ALA CA 170
+ 171 NB_1 23 ALA C 171
+ 172 NB_1 23 ALA O 172
+ 173 NB_1 23 ALA CB 173
+ 174 NB_1 24 ALA N 174
+ 175 NB_1 24 ALA CA 175
+ 176 NB_1 24 ALA C 176
+ 177 NB_1 24 ALA O 177
+ 178 NB_1 24 ALA CB 178
+ 179 NB_1 25 THR N 179
+ 180 NB_1 25 THR CA 180
+ 181 NB_1 25 THR C 181
+ 182 NB_1 25 THR O 182
+ 183 NB_1 25 THR CB 183
+ 184 NB_1 25 THR OG1 184
+ 185 NB_1 25 THR CG2 185
+ 186 NB_1 26 ALA N 186
+ 187 NB_1 26 ALA CA 187
+ 188 NB_1 26 ALA C 188
+ 189 NB_1 26 ALA O 189
+ 190 NB_1 26 ALA CB 190
+ 191 NB_1 27 GLU N 191
+ 192 NB_1 27 GLU CA 192
+ 193 NB_1 27 GLU C 193
+ 194 NB_1 27 GLU O 194
+ 195 NB_1 27 GLU CB 195
+ 196 NB_1 27 GLU CG 196
+ 197 NB_1 27 GLU CD 197
+ 198 NB_1 27 GLU OE1 198
+ 199 NB_1 27 GLU OE2 199
+ 200 NB_1 28 LYS N 200
+ 201 NB_1 28 LYS CA 201
+ 202 NB_1 28 LYS C 202
+ 203 NB_1 28 LYS O 203
+ 204 NB_1 28 LYS CB 204
+ 205 NB_1 28 LYS CG 205
+ 206 NB_1 28 LYS CD 206
+ 207 NB_1 28 LYS CE 207
+ 208 NB_1 28 LYS NZ 208
+ 209 NB_1 29 VAL N 209
+ 210 NB_1 29 VAL CA 210
+ 211 NB_1 29 VAL C 211
+ 212 NB_1 29 VAL O 212
+ 213 NB_1 29 VAL CB 213
+ 214 NB_1 29 VAL CG1 214
+ 215 NB_1 29 VAL CG2 215
+ 216 NB_1 30 PHE N 216
+ 217 NB_1 30 PHE CA 217
+ 218 NB_1 30 PHE C 218
+ 219 NB_1 30 PHE O 219
+ 220 NB_1 30 PHE CB 220
+ 221 NB_1 30 PHE CG 221
+ 222 NB_1 30 PHE CD1 222
+ 223 NB_1 30 PHE CD2 223
+ 224 NB_1 30 PHE CE1 224
+ 225 NB_1 30 PHE CE2 225
+ 226 NB_1 30 PHE CZ 226
+ 227 NB_1 31 LYS N 227
+ 228 NB_1 31 LYS CA 228
+ 229 NB_1 31 LYS C 229
+ 230 NB_1 31 LYS O 230
+ 231 NB_1 31 LYS CB 231
+ 232 NB_1 31 LYS CG 232
+ 233 NB_1 31 LYS CD 233
+ 234 NB_1 31 LYS CE 234
+ 235 NB_1 31 LYS NZ 235
+ 236 NB_1 32 GLN N 236
+ 237 NB_1 32 GLN CA 237
+ 238 NB_1 32 GLN C 238
+ 239 NB_1 32 GLN O 239
+ 240 NB_1 32 GLN CB 240
+ 241 NB_1 32 GLN CG 241
+ 242 NB_1 32 GLN CD 242
+ 243 NB_1 32 GLN OE1 243
+ 244 NB_1 32 GLN NE2 244
+ 245 NB_1 33 TYR N 245
+ 246 NB_1 33 TYR CA 246
+ 247 NB_1 33 TYR C 247
+ 248 NB_1 33 TYR O 248
+ 249 NB_1 33 TYR CB 249
+ 250 NB_1 33 TYR CG 250
+ 251 NB_1 33 TYR CD1 251
+ 252 NB_1 33 TYR CD2 252
+ 253 NB_1 33 TYR CE1 253
+ 254 NB_1 33 TYR CE2 254
+ 255 NB_1 33 TYR CZ 255
+ 256 NB_1 33 TYR OH 256
+ 257 NB_1 34 ALA N 257
+ 258 NB_1 34 ALA CA 258
+ 259 NB_1 34 ALA C 259
+ 260 NB_1 34 ALA O 260
+ 261 NB_1 34 ALA CB 261
+ 262 NB_1 35 ASN N 262
+ 263 NB_1 35 ASN CA 263
+ 264 NB_1 35 ASN C 264
+ 265 NB_1 35 ASN O 265
+ 266 NB_1 35 ASN CB 266
+ 267 NB_1 35 ASN CG 267
+ 268 NB_1 35 ASN OD1 268
+ 269 NB_1 35 ASN ND2 269
+ 270 NB_1 36 ASP N 270
+ 271 NB_1 36 ASP CA 271
+ 272 NB_1 36 ASP C 272
+ 273 NB_1 36 ASP O 273
+ 274 NB_1 36 ASP CB 274
+ 275 NB_1 36 ASP CG 275
+ 276 NB_1 36 ASP OD1 276
+ 277 NB_1 36 ASP OD2 277
+ 278 NB_1 37 ASN N 278
+ 279 NB_1 37 ASN CA 279
+ 280 NB_1 37 ASN C 280
+ 281 NB_1 37 ASN O 281
+ 282 NB_1 37 ASN CB 282
+ 283 NB_1 37 ASN CG 283
+ 284 NB_1 37 ASN OD1 284
+ 285 NB_1 37 ASN ND2 285
+ 286 NB_1 38 GLY N 286
+ 287 NB_1 38 GLY CA 287
+ 288 NB_1 38 GLY C 288
+ 289 NB_1 38 GLY O 289
+ 290 NB_1 39 VAL N 290
+ 291 NB_1 39 VAL CA 291
+ 292 NB_1 39 VAL C 292
+ 293 NB_1 39 VAL O 293
+ 294 NB_1 39 VAL CB 294
+ 295 NB_1 39 VAL CG1 295
+ 296 NB_1 39 VAL CG2 296
+ 297 NB_1 40 ASP N 297
+ 298 NB_1 40 ASP CA 298
+ 299 NB_1 40 ASP C 299
+ 300 NB_1 40 ASP O 300
+ 301 NB_1 40 ASP CB 301
+ 302 NB_1 40 ASP CG 302
+ 303 NB_1 40 ASP OD1 303
+ 304 NB_1 40 ASP OD2 304
+ 305 NB_1 41 GLY N 305
+ 306 NB_1 41 GLY CA 306
+ 307 NB_1 41 GLY C 307
+ 308 NB_1 41 GLY O 308
+ 309 NB_1 42 GLU N 309
+ 310 NB_1 42 GLU CA 310
+ 311 NB_1 42 GLU C 311
+ 312 NB_1 42 GLU O 312
+ 313 NB_1 42 GLU CB 313
+ 314 NB_1 42 GLU CG 314
+ 315 NB_1 42 GLU CD 315
+ 316 NB_1 42 GLU OE1 316
+ 317 NB_1 42 GLU OE2 317
+ 318 NB_1 43 TRP N 318
+ 319 NB_1 43 TRP CA 319
+ 320 NB_1 43 TRP C 320
+ 321 NB_1 43 TRP O 321
+ 322 NB_1 43 TRP CB 322
+ 323 NB_1 43 TRP CG 323
+ 324 NB_1 43 TRP CD1 324
+ 325 NB_1 43 TRP CD2 325
+ 326 NB_1 43 TRP NE1 326
+ 327 NB_1 43 TRP CE2 327
+ 328 NB_1 43 TRP CE3 328
+ 329 NB_1 43 TRP CZ2 329
+ 330 NB_1 43 TRP CZ3 330
+ 331 NB_1 43 TRP CH2 331
+ 332 NB_1 44 THR N 332
+ 333 NB_1 44 THR CA 333
+ 334 NB_1 44 THR C 334
+ 335 NB_1 44 THR O 335
+ 336 NB_1 44 THR CB 336
+ 337 NB_1 44 THR OG1 337
+ 338 NB_1 44 THR CG2 338
+ 339 NB_1 45 TYR N 339
+ 340 NB_1 45 TYR CA 340
+ 341 NB_1 45 TYR C 341
+ 342 NB_1 45 TYR O 342
+ 343 NB_1 45 TYR CB 343
+ 344 NB_1 45 TYR CG 344
+ 345 NB_1 45 TYR CD1 345
+ 346 NB_1 45 TYR CD2 346
+ 347 NB_1 45 TYR CE1 347
+ 348 NB_1 45 TYR CE2 348
+ 349 NB_1 45 TYR CZ 349
+ 350 NB_1 45 TYR OH 350
+ 351 NB_1 46 ASP N 351
+ 352 NB_1 46 ASP CA 352
+ 353 NB_1 46 ASP C 353
+ 354 NB_1 46 ASP O 354
+ 355 NB_1 46 ASP CB 355
+ 356 NB_1 46 ASP CG 356
+ 357 NB_1 46 ASP OD1 357
+ 358 NB_1 46 ASP OD2 358
+ 359 NB_1 47 ASP N 359
+ 360 NB_1 47 ASP CA 360
+ 361 NB_1 47 ASP C 361
+ 362 NB_1 47 ASP O 362
+ 363 NB_1 47 ASP CB 363
+ 364 NB_1 47 ASP CG 364
+ 365 NB_1 47 ASP OD1 365
+ 366 NB_1 47 ASP OD2 366
+ 367 NB_1 48 ALA N 367
+ 368 NB_1 48 ALA CA 368
+ 369 NB_1 48 ALA C 369
+ 370 NB_1 48 ALA O 370
+ 371 NB_1 48 ALA CB 371
+ 372 NB_1 49 THR N 372
+ 373 NB_1 49 THR CA 373
+ 374 NB_1 49 THR C 374
+ 375 NB_1 49 THR O 375
+ 376 NB_1 49 THR CB 376
+ 377 NB_1 49 THR OG1 377
+ 378 NB_1 49 THR CG2 378
+ 379 NB_1 50 LYS N 379
+ 380 NB_1 50 LYS CA 380
+ 381 NB_1 50 LYS C 381
+ 382 NB_1 50 LYS O 382
+ 383 NB_1 50 LYS CB 383
+ 384 NB_1 50 LYS CG 384
+ 385 NB_1 50 LYS CD 385
+ 386 NB_1 50 LYS CE 386
+ 387 NB_1 50 LYS NZ 387
+ 388 NB_1 51 THR N 388
+ 389 NB_1 51 THR CA 389
+ 390 NB_1 51 THR C 390
+ 391 NB_1 51 THR O 391
+ 392 NB_1 51 THR CB 392
+ 393 NB_1 51 THR OG1 393
+ 394 NB_1 51 THR CG2 394
+ 395 NB_1 52 PHE N 395
+ 396 NB_1 52 PHE CA 396
+ 397 NB_1 52 PHE C 397
+ 398 NB_1 52 PHE O 398
+ 399 NB_1 52 PHE CB 399
+ 400 NB_1 52 PHE CG 400
+ 401 NB_1 52 PHE CD1 401
+ 402 NB_1 52 PHE CD2 402
+ 403 NB_1 52 PHE CE1 403
+ 404 NB_1 52 PHE CE2 404
+ 405 NB_1 52 PHE CZ 405
+ 406 NB_1 53 THR N 406
+ 407 NB_1 53 THR CA 407
+ 408 NB_1 53 THR C 408
+ 409 NB_1 53 THR O 409
+ 410 NB_1 53 THR CB 410
+ 411 NB_1 53 THR OG1 411
+ 412 NB_1 53 THR CG2 412
+ 413 NB_1 54 VAL N 413
+ 414 NB_1 54 VAL CA 414
+ 415 NB_1 54 VAL C 415
+ 416 NB_1 54 VAL O 416
+ 417 NB_1 54 VAL CB 417
+ 418 NB_1 54 VAL CG1 418
+ 419 NB_1 54 VAL CG2 419
+ 420 NB_1 55 THR N 420
+ 421 NB_1 55 THR CA 421
+ 422 NB_1 55 THR C 422
+ 423 NB_1 55 THR O 423
+ 424 NB_1 55 THR CB 424
+ 425 NB_1 55 THR OG1 425
+ 426 NB_1 55 THR CG2 426
+ 427 NB_1 56 GLUT N 427
+ 428 NB_1 56 GLUT CA 428
+ 429 NB_1 56 GLUT C 429
+ 430 NB_1 56 GLUT O 430
+ 431 NB_1 56 GLUT CB 431
+ 432 NB_1 56 GLUT CG 432
+ 433 NB_1 56 GLUT CD 433
+ 434 NB_1 56 GLUT OE1 434
+ 435 NB_1 56 GLUT OE2 435
+ 436 NB_1 56 GLUT OXT 436
+
+[ bonds ]
+;ai aj func r0(nm) Kb
+ 1 2 1 1.472415023e-01 1.000000000e+04
+ 2 3 1 1.555652275e-01 1.000000000e+04
+ 2 5 1 1.536975602e-01 1.000000000e+04
+ 3 4 1 1.230634389e-01 1.000000000e+04
+ 3 9 1 1.322322956e-01 1.000000000e+04
+ 5 6 1 1.543083277e-01 1.000000000e+04
+ 6 7 1 1.750400240e-01 1.000000000e+04
+ 7 8 1 1.765628500e-01 1.000000000e+04
+ 9 10 1 1.457314311e-01 1.000000000e+04
+ 10 11 1 1.500305969e-01 1.000000000e+04
+ 10 13 1 1.520505837e-01 1.000000000e+04
+ 11 12 1 1.231440620e-01 1.000000000e+04
+ 11 16 1 1.321749598e-01 1.000000000e+04
+ 13 14 1 1.432340742e-01 1.000000000e+04
+ 13 15 1 1.533723900e-01 1.000000000e+04
+ 16 17 1 1.454038858e-01 1.000000000e+04
+ 17 18 1 1.557280001e-01 1.000000000e+04
+ 17 20 1 1.534221953e-01 1.000000000e+04
+ 18 19 1 1.246107540e-01 1.000000000e+04
+ 18 28 1 1.322377405e-01 1.000000000e+04
+ 20 21 1 1.480699835e-01 1.000000000e+04
+ 21 22 1 1.353260507e-01 1.000000000e+04
+ 21 23 1 1.391862421e-01 1.000000000e+04
+ 22 24 1 1.360158079e-01 1.000000000e+04
+ 23 25 1 1.371903058e-01 1.000000000e+04
+ 24 26 1 1.354549002e-01 1.000000000e+04
+ 25 26 1 1.404758342e-01 1.000000000e+04
+ 26 27 1 1.382084296e-01 1.000000000e+04
+ 28 29 1 1.433885979e-01 1.000000000e+04
+ 29 30 1 1.518461392e-01 1.000000000e+04
+ 29 32 1 1.548522522e-01 1.000000000e+04
+ 30 31 1 1.238197076e-01 1.000000000e+04
+ 30 37 1 1.330570179e-01 1.000000000e+04
+ 32 33 1 1.531037883e-01 1.000000000e+04
+ 33 34 1 1.527589932e-01 1.000000000e+04
+ 34 35 1 1.579746182e-01 1.000000000e+04
+ 35 36 1 1.537213388e-01 1.000000000e+04
+ 37 38 1 1.444735616e-01 1.000000000e+04
+ 38 39 1 1.573427469e-01 1.000000000e+04
+ 38 41 1 1.548887665e-01 1.000000000e+04
+ 39 40 1 1.229835761e-01 1.000000000e+04
+ 39 45 1 1.336385423e-01 1.000000000e+04
+ 41 42 1 1.562112352e-01 1.000000000e+04
+ 42 43 1 1.554952411e-01 1.000000000e+04
+ 42 44 1 1.504189815e-01 1.000000000e+04
+ 45 46 1 1.444342757e-01 1.000000000e+04
+ 46 47 1 1.536295870e-01 1.000000000e+04
+ 46 49 1 1.523529455e-01 1.000000000e+04
+ 47 48 1 1.220143024e-01 1.000000000e+04
+ 47 53 1 1.324371927e-01 1.000000000e+04
+ 49 50 1 1.528057918e-01 1.000000000e+04
+ 49 51 1 1.545754508e-01 1.000000000e+04
+ 50 52 1 1.475900064e-01 1.000000000e+04
+ 53 54 1 1.454973883e-01 1.000000000e+04
+ 54 55 1 1.517663336e-01 1.000000000e+04
+ 54 57 1 1.527327732e-01 1.000000000e+04
+ 55 56 1 1.246576913e-01 1.000000000e+04
+ 55 61 1 1.301096076e-01 1.000000000e+04
+ 57 58 1 1.531289979e-01 1.000000000e+04
+ 58 59 1 1.510767355e-01 1.000000000e+04
+ 58 60 1 1.546678376e-01 1.000000000e+04
+ 61 62 1 1.431773027e-01 1.000000000e+04
+ 62 63 1 1.528579079e-01 1.000000000e+04
+ 62 65 1 1.499292500e-01 1.000000000e+04
+ 63 64 1 1.222080194e-01 1.000000000e+04
+ 63 69 1 1.330799760e-01 1.000000000e+04
+ 65 66 1 1.495314683e-01 1.000000000e+04
+ 66 67 1 1.229172486e-01 1.000000000e+04
+ 66 68 1 1.320184078e-01 1.000000000e+04
+ 69 70 1 1.437730503e-01 1.000000000e+04
+ 70 71 1 1.530393740e-01 1.000000000e+04
+ 71 72 1 1.220852981e-01 1.000000000e+04
+ 71 73 1 1.326791996e-01 1.000000000e+04
+ 73 74 1 1.473673641e-01 1.000000000e+04
+ 74 75 1 1.518702407e-01 1.000000000e+04
+ 74 77 1 1.536864665e-01 1.000000000e+04
+ 75 76 1 1.243315728e-01 1.000000000e+04
+ 75 82 1 1.339598074e-01 1.000000000e+04
+ 77 78 1 1.492926321e-01 1.000000000e+04
+ 78 79 1 1.548927694e-01 1.000000000e+04
+ 79 80 1 1.574697749e-01 1.000000000e+04
+ 80 81 1 1.554569072e-01 1.000000000e+04
+ 82 83 1 1.468625548e-01 1.000000000e+04
+ 83 84 1 1.539028590e-01 1.000000000e+04
+ 83 86 1 1.552447745e-01 1.000000000e+04
+ 84 85 1 1.204296060e-01 1.000000000e+04
+ 84 89 1 1.337607192e-01 1.000000000e+04
+ 86 87 1 1.426505170e-01 1.000000000e+04
+ 86 88 1 1.510561485e-01 1.000000000e+04
+ 89 90 1 1.451563984e-01 1.000000000e+04
+ 90 91 1 1.530166984e-01 1.000000000e+04
+ 90 93 1 1.508889327e-01 1.000000000e+04
+ 91 92 1 1.226869186e-01 1.000000000e+04
+ 91 97 1 1.327627960e-01 1.000000000e+04
+ 93 94 1 1.530745570e-01 1.000000000e+04
+ 94 95 1 1.543596126e-01 1.000000000e+04
+ 94 96 1 1.503105452e-01 1.000000000e+04
+ 97 98 1 1.463456866e-01 1.000000000e+04
+ 98 99 1 1.548773386e-01 1.000000000e+04
+ 98 101 1 1.535019870e-01 1.000000000e+04
+ 99 100 1 1.213922568e-01 1.000000000e+04
+ 99 106 1 1.328316227e-01 1.000000000e+04
+ 101 102 1 1.560920562e-01 1.000000000e+04
+ 102 103 1 1.511972883e-01 1.000000000e+04
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+
+[ system ]
+; name
+ Macromolecule
+
+[ molecules ]
+; name #molec
+ Macromolecule 1
diff --git a/user-doc/tutorials/lugano-6d/GB1_start.gro b/user-doc/tutorials/lugano-6d/GB1_start.gro
new file mode 100644
index 0000000000000000000000000000000000000000..ad24d946a641e19f69d80c5feb0af222766e8b32
--- /dev/null
+++ b/user-doc/tutorials/lugano-6d/GB1_start.gro
@@ -0,0 +1,439 @@
+Macromolecule
+ 436
+ 1MET N 1 7.844 5.566 6.747 -2.3362 1.5726 -0.8609
+ 1MET CA 2 7.779 5.665 6.834 -1.0966 -0.0189 2.0550
+ 1MET C 3 7.722 5.609 6.967 0.2595 -1.4984 2.0401
+ 1MET O 4 7.653 5.510 6.940 1.0077 -2.0144 1.9982
+ 1MET CB 5 7.685 5.725 6.727 0.5198 -1.2593 -0.1428
+ 1MET CG 6 7.562 5.650 6.672 -0.9066 0.8777 0.0149
+ 1MET SD 7 7.456 5.567 6.784 0.3641 -1.1195 -0.1999
+ 1MET CE 8 7.388 5.725 6.824 0.0658 -0.6517 -2.3917
+ 2THR N 9 7.761 5.662 7.082 -0.1928 1.4721 0.9193
+ 2THR CA 10 7.739 5.601 7.212 0.3130 -1.6993 -0.3781
+ 2THR C 11 7.872 5.628 7.276 -0.3172 0.7299 -0.0150
+ 2THR O 12 7.993 5.609 7.268 0.0285 1.3340 2.6765
+ 2THR CB 13 7.725 5.450 7.194 -0.2454 -1.7436 0.3667
+ 2THR OG1 14 7.588 5.412 7.178 -0.8774 0.6937 -0.5124
+ 2THR CG2 15 7.803 5.350 7.280 1.5840 -1.6191 -1.0890
+ 3TYR N 16 7.854 5.601 7.404 1.5585 -0.6784 -0.0153
+ 3TYR CA 17 7.949 5.536 7.493 1.2615 -0.1722 0.6854
+ 3TYR C 18 7.878 5.493 7.624 0.2837 -0.9376 -0.0830
+ 3TYR O 19 7.753 5.501 7.620 0.1968 -1.4186 1.0626
+ 3TYR CB 20 8.060 5.640 7.470 0.2624 0.6211 -0.6835
+ 3TYR CG 21 8.162 5.572 7.387 1.1745 -0.1790 1.0337
+ 3TYR CD1 22 8.145 5.451 7.328 -0.1129 0.5882 -0.2473
+ 3TYR CD2 23 8.274 5.647 7.354 -0.2462 1.7159 0.2959
+ 3TYR CE1 24 8.242 5.400 7.248 -0.5015 0.2813 -0.5313
+ 3TYR CE2 25 8.385 5.587 7.300 -1.6810 -0.2947 -0.5489
+ 3TYR CZ 26 8.364 5.460 7.244 0.2631 -1.1369 0.5046
+ 3TYR OH 27 8.466 5.376 7.204 0.8998 -1.0942 2.0016
+ 4LYS N 28 7.936 5.414 7.713 -1.2086 -0.7318 1.1334
+ 4LYS CA 29 7.880 5.413 7.845 0.4770 0.0713 1.8845
+ 4LYS C 30 7.985 5.493 7.920 0.4307 1.5420 0.4444
+ 4LYS O 31 8.086 5.542 7.867 0.7280 -0.7433 -1.2517
+ 4LYS CB 32 7.890 5.263 7.881 0.7516 -0.3529 0.1295
+ 4LYS CG 33 7.941 5.230 8.021 1.4955 -0.2498 -0.1104
+ 4LYS CD 34 7.908 5.083 8.044 0.1879 -0.1553 -1.2480
+ 4LYS CE 35 7.842 5.023 7.914 0.7972 1.1486 -2.1770
+ 4LYS NZ 36 7.901 4.894 7.854 -0.2581 0.1619 -1.1353
+ 5LEU N 37 7.893 5.544 8.000 -1.7002 0.3311 -1.1285
+ 5LEU CA 38 7.888 5.675 8.061 0.7849 -0.1114 0.1466
+ 5LEU C 39 7.742 5.732 8.045 0.4405 -0.8830 0.4977
+ 5LEU O 40 7.726 5.810 7.951 0.7680 0.9162 1.8596
+ 5LEU CB 41 7.993 5.771 7.999 -0.6557 1.0224 -0.5925
+ 5LEU CG 42 7.971 5.920 8.042 0.1169 0.9716 0.0010
+ 5LEU CD1 43 8.060 6.004 7.947 1.2407 0.5270 0.6480
+ 5LEU CD2 44 7.829 5.967 8.027 -0.3853 -0.5565 -0.2622
+ 6ILE N 45 7.642 5.706 8.129 -0.3597 -0.6462 -0.3749
+ 6ILE CA 46 7.510 5.765 8.135 0.5206 1.4523 -0.8318
+ 6ILE C 47 7.432 5.640 8.178 1.4621 1.1980 0.1925
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+ 6ILE CG2 51 7.563 5.659 7.899 1.2379 0.2681 -2.2815
+ 6ILE CD1 52 7.329 5.785 7.807 0.4974 1.6562 -1.7875
+ 7LEU N 53 7.354 5.656 8.283 -0.1887 -1.1031 -0.5943
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+ 7LEU CD2 60 7.039 5.968 8.320 -2.6758 -0.5525 0.0125
+ 8ASN N 61 7.116 5.572 8.064 0.8759 -0.5013 -1.0766
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+ 15GLU O 113 5.695 5.682 6.528 0.0322 -0.2893 -0.9631
+ 15GLU CB 114 5.447 5.781 6.728 -0.5909 -0.4072 -1.7490
+ 15GLU CG 115 5.337 5.693 6.698 -0.9582 0.2213 -2.2667
+ 15GLU CD 116 5.209 5.772 6.705 -1.9186 -1.4236 -0.5129
+ 15GLU OE1 117 5.150 5.783 6.817 -0.2963 -0.3658 0.2877
+ 15GLU OE2 118 5.219 5.874 6.631 0.9736 -1.2418 -0.0087
+ 16THR N 119 5.496 5.784 6.528 0.6396 -0.1330 0.3241
+ 16THR CA 120 5.526 5.853 6.400 1.7718 2.0551 1.7093
+ 16THR C 121 5.411 5.842 6.303 1.3386 0.6129 2.3482
+ 16THR O 122 5.296 5.843 6.351 0.2982 -1.0022 0.0264
+ 16THR CB 123 5.641 5.794 6.321 -0.5348 -1.3735 0.6993
+ 16THR OG1 124 5.669 5.869 6.203 -1.1371 -2.7706 -0.3667
+ 16THR CG2 125 5.625 5.653 6.318 0.8109 -1.5385 0.6582
+ 17THR N 126 5.407 5.889 6.180 -1.3959 0.3390 2.2878
+ 17THR CA 127 5.274 5.908 6.127 -0.9944 -0.7968 0.7942
+ 17THR C 128 5.189 5.808 6.053 -0.2776 0.1971 -1.4808
+ 17THR O 129 5.073 5.793 6.089 0.7520 0.6417 2.5098
+ 17THR CB 130 5.242 6.043 6.060 1.8480 0.1109 1.1448
+ 17THR OG1 131 5.367 6.082 6.006 0.3468 0.1491 -2.5488
+ 17THR CG2 132 5.202 6.167 6.138 1.5067 0.3032 0.6635
+ 18THR N 133 5.245 5.804 5.935 2.0899 0.1538 -0.4178
+ 18THR CA 134 5.239 5.698 5.837 0.8771 -0.0357 -0.1527
+ 18THR C 135 5.254 5.721 5.686 -0.2997 0.6959 -0.1659
+ 18THR O 136 5.368 5.757 5.662 -1.3212 4.2815 -0.2861
+ 18THR CB 137 5.109 5.612 5.872 0.1408 0.6261 -1.1896
+ 18THR OG1 138 5.099 5.514 5.769 -0.0258 -0.5809 -0.0599
+ 18THR CG2 139 4.992 5.717 5.877 -1.0085 -0.6681 -0.2223
+ 19GLU N 140 5.191 5.647 5.597 -1.0180 -0.3266 1.1539
+ 19GLU CA 141 5.250 5.652 5.464 0.4196 -2.0175 1.6885
+ 19GLU C 142 5.154 5.570 5.382 0.4561 -0.8189 0.4108
+ 19GLU O 143 5.087 5.510 5.466 -0.7449 0.7137 0.5985
+ 19GLU CB 144 5.395 5.608 5.452 1.5309 1.7056 -0.5557
+ 19GLU CG 145 5.433 5.666 5.323 0.8855 2.7050 -0.3078
+ 19GLU CD 146 5.546 5.605 5.247 0.5748 -0.1570 1.3678
+ 19GLU OE1 147 5.581 5.485 5.253 -1.7734 -0.9744 0.0444
+ 19GLU OE2 148 5.643 5.685 5.270 0.9466 -0.6246 1.4365
+ 20ALA N 149 5.125 5.647 5.278 -1.8351 -1.3774 0.5867
+ 20ALA CA 150 5.008 5.721 5.232 -1.2832 -1.0651 -0.3522
+ 20ALA C 151 4.996 5.653 5.097 0.2751 -0.9114 -0.5840
+ 20ALA O 152 5.090 5.577 5.069 0.6716 -1.0837 1.0735
+ 20ALA CB 153 5.009 5.873 5.248 1.5626 -1.2488 2.3068
+ 21VAL N 154 4.876 5.673 5.047 -0.1318 1.5524 1.1566
+ 21VAL CA 155 4.812 5.618 4.928 0.4549 1.0228 1.0785
+ 21VAL C 156 4.776 5.473 4.955 -0.9418 1.3015 0.8299
+ 21VAL O 157 4.779 5.397 4.859 -1.7551 0.2794 1.5919
+ 21VAL CB 158 4.913 5.643 4.813 0.5236 -0.2946 0.8437
+ 21VAL CG1 159 4.824 5.726 4.707 1.6428 1.2955 1.1080
+ 21VAL CG2 160 5.044 5.717 4.849 0.7692 -0.2881 -0.0377
+ 22ASP N 161 4.679 5.481 5.047 -1.3468 0.4829 0.4817
+ 22ASP CA 162 4.692 5.401 5.167 -0.7576 0.6815 0.5555
+ 22ASP C 163 4.592 5.292 5.204 0.3246 -1.1202 -1.5754
+ 22ASP O 164 4.471 5.299 5.199 0.3863 -0.0693 -1.6501
+ 22ASP CB 165 4.711 5.494 5.287 -0.3091 -0.6993 1.5862
+ 22ASP CG 166 4.680 5.641 5.261 1.3243 -0.5583 0.2838
+ 22ASP OD1 167 4.694 5.676 5.144 -0.2202 -0.3225 0.1495
+ 22ASP OD2 168 4.580 5.681 5.319 0.3270 -3.0487 0.4233
+ 23ALA N 169 4.643 5.177 5.245 -1.4012 -1.7806 -1.1916
+ 23ALA CA 170 4.543 5.074 5.260 -1.6755 -1.7067 -2.4264
+ 23ALA C 171 4.482 5.051 5.395 1.0362 1.0470 -0.6031
+ 23ALA O 172 4.499 4.937 5.427 0.1624 0.8659 -0.7682
+ 23ALA CB 173 4.575 4.942 5.192 0.0633 -1.8321 -1.4051
+ 24ALA N 174 4.385 5.113 5.459 -0.2463 -0.3974 -1.0852
+ 24ALA CA 175 4.386 5.075 5.600 -0.9951 1.1665 -0.6252
+ 24ALA C 176 4.281 4.984 5.661 -0.3156 0.2400 -0.8121
+ 24ALA O 177 4.225 5.013 5.769 0.4482 1.8577 -0.8319
+ 24ALA CB 178 4.418 5.207 5.670 -1.6745 1.9391 -1.7414
+ 25THR N 179 4.220 4.937 5.554 1.1591 0.9565 -1.9953
+ 25THR CA 180 4.081 4.919 5.520 0.9262 0.0209 -0.6217
+ 25THR C 181 4.024 4.797 5.589 0.0467 0.0773 -1.2249
+ 25THR O 182 4.077 4.687 5.612 1.0262 0.5229 -1.3115
+ 25THR CB 183 4.091 4.901 5.368 -1.5591 1.1193 -0.9657
+ 25THR OG1 184 4.074 5.037 5.326 -0.7875 1.3169 -0.6516
+ 25THR CG2 185 3.947 4.871 5.343 -1.7386 2.1988 -1.2716
+ 26ALA N 186 3.892 4.807 5.609 0.0336 0.0325 -1.2922
+ 26ALA CA 187 3.788 4.708 5.636 0.6497 -0.2623 0.1103
+ 26ALA C 188 3.717 4.695 5.497 0.0550 0.9466 0.2918
+ 26ALA O 189 3.675 4.585 5.458 0.1765 0.9023 0.2892
+ 26ALA CB 190 3.691 4.749 5.745 -0.6643 0.2568 -1.2150
+ 27GLU N 191 3.729 4.765 5.384 0.9111 -2.2676 -1.7540
+ 27GLU CA 192 3.612 4.776 5.296 -1.5823 -0.5323 1.5220
+ 27GLU C 193 3.647 4.776 5.146 -1.0408 0.7918 1.6328
+ 27GLU O 194 3.648 4.667 5.094 -1.3616 0.6462 1.9260
+ 27GLU CB 195 3.513 4.878 5.348 -1.7315 -0.0572 0.3506
+ 27GLU CG 196 3.374 4.831 5.320 -1.3926 -0.6643 -0.3440
+ 27GLU CD 197 3.290 4.918 5.231 -1.9663 -0.6530 0.1966
+ 27GLU OE1 198 3.174 4.879 5.226 -1.3318 -2.5232 -1.0809
+ 27GLU OE2 199 3.375 4.941 5.145 -1.8532 -0.1499 0.4402
+ 28LYS N 200 3.630 4.889 5.079 -1.0828 0.0053 0.2874
+ 28LYS CA 201 3.627 4.924 4.937 0.4997 1.4483 0.5731
+ 28LYS C 202 3.649 4.787 4.874 -1.4446 1.0306 0.7421
+ 28LYS O 203 3.585 4.741 4.779 1.5890 -2.5788 0.2566
+ 28LYS CB 204 3.695 5.058 4.907 1.7191 0.6867 -0.1633
+ 28LYS CG 205 3.657 5.112 4.775 -1.2925 -1.3208 -0.2116
+ 28LYS CD 206 3.537 5.210 4.798 -2.4613 -2.3707 -1.6497
+ 28LYS CE 207 3.511 5.256 4.649 -1.5725 1.5512 -0.7156
+ 28LYS NZ 208 3.362 5.272 4.620 -2.0766 -0.5177 0.5144
+ 29VAL N 209 3.758 4.729 4.919 -0.0470 2.0361 -1.2425
+ 29VAL CA 210 3.777 4.600 4.859 0.6892 -0.1042 3.2054
+ 29VAL C 211 3.659 4.508 4.819 1.8605 0.1842 -1.5721
+ 29VAL O 212 3.570 4.532 4.737 -1.2046 -1.8372 0.9039
+ 29VAL CB 213 3.903 4.508 4.852 0.8979 0.2835 1.1015
+ 29VAL CG1 214 3.875 4.364 4.899 1.2565 -0.5825 -1.2102
+ 29VAL CG2 215 3.995 4.513 4.745 -0.5411 -0.6538 -0.2280
+ 30PHE N 216 3.641 4.387 4.875 0.6214 1.0546 0.0074
+ 30PHE CA 217 3.607 4.282 4.776 1.3208 1.4668 -0.6851
+ 30PHE C 218 3.488 4.322 4.687 -0.5437 0.7113 1.3713
+ 30PHE O 219 3.400 4.238 4.702 -0.4305 -0.4926 -3.2513
+ 30PHE CB 220 3.576 4.166 4.871 0.6514 1.7368 -0.5664
+ 30PHE CG 221 3.685 4.157 4.978 -1.3034 -1.3005 1.3317
+ 30PHE CD1 222 3.674 4.250 5.082 -0.0017 1.6205 -0.9873
+ 30PHE CD2 223 3.777 4.054 4.994 -0.9745 -1.2531 -0.0770
+ 30PHE CE1 224 3.764 4.245 5.192 -1.7808 0.3320 0.4888
+ 30PHE CE2 225 3.861 4.050 5.105 -0.7789 -1.0945 -0.2178
+ 30PHE CZ 226 3.848 4.138 5.204 0.1362 1.3895 -2.1886
+ 31LYS N 227 3.502 4.373 4.566 0.5005 0.0973 1.2156
+ 31LYS CA 228 3.395 4.436 4.492 1.1684 -1.5989 -1.2924
+ 31LYS C 229 3.481 4.519 4.394 0.5733 -0.0715 -0.5503
+ 31LYS O 230 3.432 4.631 4.383 -0.5770 -0.4826 0.2463
+ 31LYS CB 231 3.285 4.507 4.567 1.6371 -1.7181 -0.4831
+ 31LYS CG 232 3.343 4.555 4.695 -0.8168 -0.1298 0.0892
+ 31LYS CD 233 3.404 4.689 4.724 0.1013 -0.6254 0.4515
+ 31LYS CE 234 3.389 4.741 4.869 0.2328 -0.0831 0.2725
+ 31LYS NZ 235 3.335 4.882 4.869 -0.1103 -0.2145 -0.1019
+ 32GLN N 236 3.605 4.477 4.365 0.8626 0.3675 0.0289
+ 32GLN CA 237 3.699 4.578 4.314 -0.9037 1.3837 -1.2951
+ 32GLN C 238 3.811 4.533 4.229 -0.4614 -0.2167 0.0914
+ 32GLN O 239 3.921 4.571 4.253 -1.0213 1.4598 0.0912
+ 32GLN CB 240 3.784 4.655 4.413 -0.0071 -0.5270 -0.5294
+ 32GLN CG 241 3.690 4.753 4.473 0.1742 0.2837 -1.5400
+ 32GLN CD 242 3.760 4.819 4.587 1.3721 -0.7684 -1.6542
+ 32GLN OE1 243 3.856 4.770 4.648 1.5242 0.5910 -0.7665
+ 32GLN NE2 244 3.807 4.932 4.530 -0.0972 0.7043 -0.0459
+ 33TYR N 245 3.795 4.461 4.120 1.4671 0.4256 -0.6518
+ 33TYR CA 246 3.815 4.517 3.987 0.2687 -1.0173 -1.4780
+ 33TYR C 247 3.912 4.636 3.972 -0.2788 -0.1522 1.3109
+ 33TYR O 248 4.027 4.634 3.927 -1.2768 0.8835 -1.5357
+ 33TYR CB 249 3.681 4.573 3.940 -0.0169 -0.4332 -0.0175
+ 33TYR CG 250 3.592 4.460 3.898 -0.1165 0.2348 -1.6803
+ 33TYR CD1 251 3.530 4.371 3.988 0.5090 0.2376 -1.2389
+ 33TYR CD2 252 3.569 4.427 3.766 -0.5407 -0.9083 -1.3371
+ 33TYR CE1 253 3.433 4.267 3.966 -0.0329 0.3214 0.5681
+ 33TYR CE2 254 3.481 4.321 3.738 -0.5429 -1.5466 0.8722
+ 33TYR CZ 255 3.415 4.241 3.830 -1.5822 -0.6549 0.9328
+ 33TYR OH 256 3.317 4.166 3.768 -0.7697 -0.6368 -0.4215
+ 34ALA N 257 3.834 4.740 3.942 1.1650 0.9429 1.2598
+ 34ALA CA 258 3.851 4.876 3.893 -0.0557 0.1294 -1.6208
+ 34ALA C 259 3.963 4.874 3.792 0.4871 -1.4113 -1.0124
+ 34ALA O 260 3.958 4.795 3.699 -0.6367 -0.8211 -1.4786
+ 34ALA CB 261 3.802 4.991 3.982 -1.1805 -0.7081 -1.1443
+ 35ASN N 262 4.077 4.934 3.818 0.0396 -1.0340 0.1176
+ 35ASN CA 263 4.184 4.911 3.726 -0.3061 -1.4790 -0.1757
+ 35ASN C 264 4.265 4.815 3.816 -0.2693 -0.0217 1.3825
+ 35ASN O 265 4.361 4.862 3.871 0.4430 0.0138 0.1462
+ 35ASN CB 266 4.267 5.032 3.688 0.5801 -1.5238 1.5191
+ 35ASN CG 267 4.293 5.109 3.813 -0.0550 1.5248 -0.1185
+ 35ASN OD1 268 4.202 5.112 3.896 -1.1978 0.5730 -1.2937
+ 35ASN ND2 269 4.388 5.201 3.808 0.2881 1.4627 3.0450
+ 36ASP N 270 4.264 4.685 3.830 -1.2263 -0.2259 -0.2726
+ 36ASP CA 271 4.373 4.602 3.879 -0.6680 0.7379 0.1544
+ 36ASP C 272 4.399 4.460 3.828 -0.0361 1.1024 -0.5513
+ 36ASP O 273 4.440 4.370 3.902 -0.0205 0.4264 -1.3573
+ 36ASP CB 274 4.399 4.638 4.025 -0.7572 -2.7619 1.1243
+ 36ASP CG 275 4.274 4.682 4.102 -0.0809 1.6679 -0.0691
+ 36ASP OD1 276 4.225 4.593 4.173 -0.8650 2.1707 0.0294
+ 36ASP OD2 277 4.205 4.771 4.053 -0.1892 3.2885 2.7766
+ 37ASN N 278 4.322 4.442 3.721 0.1433 -0.4612 -0.4415
+ 37ASN CA 279 4.329 4.322 3.639 -0.9804 -0.4537 -0.5681
+ 37ASN C 280 4.458 4.347 3.558 -0.5768 -1.2896 -0.1969
+ 37ASN O 281 4.503 4.270 3.475 0.3800 -1.0257 0.0613
+ 37ASN CB 282 4.222 4.273 3.543 -0.7021 -2.5238 0.1233
+ 37ASN CG 283 4.079 4.270 3.599 -0.8705 1.5891 0.2128
+ 37ASN OD1 284 3.992 4.180 3.596 0.5608 0.1699 -0.3461
+ 37ASN ND2 285 4.047 4.382 3.662 -0.6117 1.2246 1.0132
+ 38GLY N 286 4.497 4.473 3.578 0.6894 -1.6512 -0.3122
+ 38GLY CA 287 4.502 4.575 3.476 -2.4268 -1.0090 0.0761
+ 38GLY C 288 4.518 4.548 3.325 -0.7013 0.1719 0.0192
+ 38GLY O 289 4.585 4.630 3.266 -0.6024 0.9672 1.1819
+ 39VAL N 290 4.475 4.431 3.281 0.5101 -0.8931 1.5408
+ 39VAL CA 291 4.555 4.327 3.221 0.9942 -0.0876 0.7586
+ 39VAL C 292 4.679 4.347 3.137 -1.0732 -0.1321 -2.4663
+ 39VAL O 293 4.721 4.461 3.114 1.3533 -0.2749 0.6104
+ 39VAL CB 294 4.446 4.248 3.153 -0.2127 0.1295 2.3863
+ 39VAL CG1 295 4.306 4.258 3.206 -0.6753 2.0865 0.9212
+ 39VAL CG2 296 4.486 4.309 3.028 0.0344 -1.0010 1.8985
+ 40ASP N 297 4.719 4.245 3.062 2.1191 0.4792 -1.7432
+ 40ASP CA 298 4.761 4.272 2.928 1.2839 -0.8486 -2.2932
+ 40ASP C 299 4.755 4.142 2.849 1.0107 -0.8388 -2.2876
+ 40ASP O 300 4.676 4.142 2.755 -1.2703 -3.4183 -0.5197
+ 40ASP CB 301 4.883 4.360 2.948 0.1645 0.2776 0.0533
+ 40ASP CG 302 4.925 4.419 2.816 -1.1528 0.3488 -0.3443
+ 40ASP OD1 303 4.830 4.493 2.773 -2.8758 -1.1448 0.7324
+ 40ASP OD2 304 5.035 4.438 2.759 -1.6064 -1.1930 -1.8674
+ 41GLY N 305 4.799 4.031 2.904 -1.3091 0.0011 1.6550
+ 41GLY CA 306 4.734 3.913 2.850 0.4362 0.5549 -1.9094
+ 41GLY C 307 4.790 3.789 2.781 1.2629 -0.0457 -0.2048
+ 41GLY O 308 4.907 3.795 2.742 0.3556 0.8889 -3.0448
+ 42GLU N 309 4.709 3.689 2.817 1.8116 -0.5333 -0.3067
+ 42GLU CA 310 4.755 3.549 2.816 -0.7146 -1.4268 -1.0165
+ 42GLU C 311 4.650 3.511 2.716 -1.4350 0.3938 -0.9933
+ 42GLU O 312 4.567 3.427 2.740 -0.6877 0.0016 0.3204
+ 42GLU CB 313 4.707 3.516 2.954 -0.4814 0.2128 -0.5213
+ 42GLU CG 314 4.818 3.482 3.043 -0.5799 -1.3586 -0.9773
+ 42GLU CD 315 4.958 3.528 2.994 -0.7537 -0.6413 -0.8061
+ 42GLU OE1 316 5.028 3.589 3.084 -1.5540 -0.8967 -0.0007
+ 42GLU OE2 317 5.028 3.431 2.945 -0.1668 -0.3416 -0.5738
+ 43TRP N 318 4.643 3.585 2.608 -0.0818 -0.3557 -1.6268
+ 43TRP CA 319 4.533 3.594 2.511 -1.2938 -0.8785 -0.3320
+ 43TRP C 320 4.410 3.512 2.516 -1.0157 -1.4069 -1.7880
+ 43TRP O 321 4.392 3.399 2.471 -2.8227 -1.5398 -0.8353
+ 43TRP CB 322 4.607 3.576 2.379 0.7839 0.0108 0.6590
+ 43TRP CG 323 4.664 3.436 2.370 -0.2715 -0.3477 -0.7465
+ 43TRP CD1 324 4.631 3.304 2.344 -1.2422 0.2775 -2.9821
+ 43TRP CD2 325 4.774 3.415 2.457 0.1405 0.5616 -1.0342
+ 43TRP NE1 326 4.727 3.212 2.380 -1.4679 1.3981 0.9238
+ 43TRP CE2 327 4.816 3.280 2.458 -1.7599 -0.1494 2.6878
+ 43TRP CE3 328 4.840 3.523 2.520 1.6895 -0.6653 -0.4782
+ 43TRP CZ2 329 4.930 3.242 2.526 0.0328 -0.5255 -0.3175
+ 43TRP CZ3 330 4.945 3.477 2.596 0.6181 -1.4481 0.5704
+ 43TRP CH2 331 4.983 3.339 2.606 1.5208 -1.2827 -0.3492
+ 44THR N 332 4.285 3.552 2.538 -0.2411 -0.5761 1.6733
+ 44THR CA 333 4.196 3.447 2.490 -0.8311 0.4269 0.5152
+ 44THR C 334 4.139 3.496 2.358 1.4269 0.2335 -0.5735
+ 44THR O 335 4.095 3.412 2.277 0.6988 1.2683 -1.2753
+ 44THR CB 336 4.093 3.384 2.580 -0.5048 1.1653 1.4150
+ 44THR OG1 337 4.015 3.291 2.508 1.1703 1.9353 -1.5795
+ 44THR CG2 338 4.063 3.454 2.710 0.8194 -0.2892 2.5372
+ 45TYR N 339 4.132 3.631 2.354 -0.6671 0.1646 -0.4451
+ 45TYR CA 340 4.072 3.701 2.241 -0.6786 0.1235 -0.4639
+ 45TYR C 341 3.942 3.769 2.280 -0.3870 0.8785 -0.7932
+ 45TYR O 342 3.884 3.762 2.388 -0.3675 1.4124 -0.7481
+ 45TYR CB 343 4.069 3.637 2.105 -0.5994 1.1310 -0.9449
+ 45TYR CG 344 4.156 3.721 2.009 1.1039 1.0605 0.4692
+ 45TYR CD1 345 4.069 3.813 1.948 -0.8605 -0.3350 1.0560
+ 45TYR CD2 346 4.282 3.682 1.960 -0.7149 -3.1509 -1.3635
+ 45TYR CE1 347 4.122 3.899 1.857 -0.7670 -0.1525 1.2823
+ 45TYR CE2 348 4.327 3.765 1.859 -0.4066 -0.6498 0.7211
+ 45TYR CZ 349 4.255 3.880 1.825 -0.8501 -0.7577 1.2913
+ 45TYR OH 350 4.326 3.940 1.723 -2.6472 -1.4269 -0.4221
+ 46ASP N 351 3.871 3.836 2.190 -1.0397 -0.2606 -1.1458
+ 46ASP CA 352 3.773 3.936 2.228 0.1962 0.5100 0.0700
+ 46ASP C 353 3.751 3.986 2.372 0.5539 0.5102 0.1242
+ 46ASP O 354 3.683 4.087 2.389 -0.1937 0.2836 -1.4303
+ 46ASP CB 355 3.635 3.887 2.189 0.5059 -0.3314 0.0164
+ 46ASP CG 356 3.643 3.837 2.047 1.2329 0.8247 -0.3619
+ 46ASP OD1 357 3.744 3.769 2.020 1.0518 0.3658 0.1091
+ 46ASP OD2 358 3.577 3.876 1.947 0.1638 -0.7160 -0.2867
+ 47ASP N 359 3.826 3.944 2.472 -0.4026 -1.7850 -0.0693
+ 47ASP CA 360 3.870 4.016 2.590 0.8484 0.6365 -1.9346
+ 47ASP C 361 3.959 4.138 2.582 0.2307 1.3127 0.6874
+ 47ASP O 362 4.016 4.167 2.477 -1.5146 0.7016 -0.4721
+ 47ASP CB 363 3.931 3.915 2.684 0.2383 1.0442 -1.0888
+ 47ASP CG 364 4.057 3.855 2.631 -1.1082 -1.7099 -1.3354
+ 47ASP OD1 365 4.158 3.883 2.702 -0.2783 2.1742 -3.7664
+ 47ASP OD2 366 4.101 3.909 2.528 0.5220 -1.5201 -0.5779
+ 48ALA N 367 3.959 4.234 2.675 0.1709 -0.5630 2.7282
+ 48ALA CA 368 4.057 4.338 2.650 -0.2165 -0.2490 2.5112
+ 48ALA C 369 4.124 4.414 2.767 -0.0290 0.6865 1.8093
+ 48ALA O 370 4.163 4.355 2.868 0.7108 -0.8032 0.6892
+ 48ALA CB 371 3.992 4.444 2.563 0.7766 -2.1540 -0.7564
+ 49THR N 372 4.105 4.544 2.781 0.5822 1.1256 -0.9439
+ 49THR CA 373 4.135 4.617 2.902 0.8540 -1.6135 0.7211
+ 49THR C 374 4.070 4.561 3.025 -0.1875 -0.7500 0.5809
+ 49THR O 375 4.111 4.604 3.130 0.6347 1.1345 -0.4757
+ 49THR CB 376 4.121 4.767 2.901 1.3806 -1.5525 -0.7724
+ 49THR OG1 377 4.062 4.803 2.776 -0.4003 1.6892 0.8759
+ 49THR CG2 378 4.255 4.813 2.953 1.4767 0.4750 -2.6967
+ 50LYS N 379 3.941 4.531 3.015 -0.4473 0.7314 -0.8447
+ 50LYS CA 380 3.870 4.476 3.129 0.4677 -2.0666 -1.5312
+ 50LYS C 381 3.727 4.456 3.083 -0.4756 1.1996 -0.3315
+ 50LYS O 382 3.649 4.552 3.089 -1.9475 -0.0361 2.1806
+ 50LYS CB 383 3.876 4.569 3.253 1.0238 -0.2003 -2.9017
+ 50LYS CG 384 3.788 4.702 3.247 1.5875 0.3625 -0.1995
+ 50LYS CD 385 3.776 4.757 3.384 1.1792 0.0886 -0.1221
+ 50LYS CE 386 3.691 4.874 3.424 -0.6768 -1.5347 0.8294
+ 50LYS NZ 387 3.714 4.969 3.312 -1.9675 0.9057 2.5343
+ 51THR N 388 3.699 4.342 3.022 -0.0193 0.4876 0.7515
+ 51THR CA 389 3.571 4.277 3.043 -0.0162 0.3676 0.4040
+ 51THR C 390 3.451 4.370 3.046 0.8195 1.5778 -1.6581
+ 51THR O 391 3.441 4.465 3.125 -1.3383 1.9259 -2.2687
+ 51THR CB 392 3.581 4.218 3.180 -0.4419 0.2637 0.3937
+ 51THR OG1 393 3.457 4.189 3.244 -0.1908 -0.6275 0.4878
+ 51THR CG2 394 3.674 4.322 3.235 1.1387 -0.8336 -0.1088
+ 52PHE N 395 3.335 4.361 2.981 -1.5557 0.0665 2.3634
+ 52PHE CA 396 3.244 4.474 2.959 -0.7138 0.3966 0.2856
+ 52PHE C 397 3.163 4.430 3.080 -0.1201 0.3059 0.6530
+ 52PHE O 398 3.055 4.486 3.112 0.7463 3.0924 -0.9678
+ 52PHE CB 399 3.138 4.447 2.853 -0.0613 -0.3332 -0.2020
+ 52PHE CG 400 3.169 4.390 2.723 0.9187 -0.0845 -0.0860
+ 52PHE CD1 401 3.270 4.448 2.646 0.7567 -0.1741 -0.3669
+ 52PHE CD2 402 3.089 4.292 2.665 0.2434 -0.1766 0.9739
+ 52PHE CE1 403 3.268 4.400 2.514 0.4798 1.1856 -0.8683
+ 52PHE CE2 404 3.087 4.241 2.529 2.8801 -1.1424 1.2424
+ 52PHE CZ 405 3.172 4.318 2.459 0.5003 0.5254 0.0576
+ 53THR N 406 3.235 4.370 3.173 -0.6904 0.6297 1.3076
+ 53THR CA 407 3.174 4.363 3.305 -1.9534 -0.2712 0.7023
+ 53THR C 408 3.194 4.486 3.393 -0.1545 -0.5365 0.7218
+ 53THR O 409 3.308 4.523 3.413 0.4866 -0.9861 -1.8553
+ 53THR CB 410 3.177 4.248 3.408 -0.2648 -0.4948 0.4466
+ 53THR OG1 411 3.309 4.257 3.465 -0.2161 -1.1958 0.4466
+ 53THR CG2 412 3.132 4.124 3.337 -3.4434 0.3828 0.7719
+ 54VAL N 413 3.097 4.579 3.396 -0.2514 -0.5841 -0.4915
+ 54VAL CA 414 3.134 4.715 3.428 -1.5466 -0.1050 -0.9519
+ 54VAL C 415 3.067 4.770 3.556 1.3182 -0.1569 0.6504
+ 54VAL O 416 3.119 4.846 3.639 -0.5489 1.3459 0.5180
+ 54VAL CB 417 3.138 4.823 3.313 0.0611 1.3754 0.4445
+ 54VAL CG1 418 3.101 4.967 3.361 1.4731 1.4593 1.3524
+ 54VAL CG2 419 3.287 4.842 3.272 0.6921 1.1369 2.5168
+ 55THR N 420 2.936 4.755 3.557 1.1639 1.0835 0.7063
+ 55THR CA 421 2.858 4.763 3.680 -1.2771 0.1129 -0.6899
+ 55THR C 422 2.780 4.889 3.714 -1.5856 0.1686 -1.5788
+ 55THR O 423 2.693 4.906 3.798 1.1921 -0.8574 1.7814
+ 55THR CB 424 2.911 4.669 3.787 0.0642 -0.0255 -1.4524
+ 55THR OG1 425 3.001 4.570 3.742 1.0641 0.0621 0.2631
+ 55THR CG2 426 2.786 4.580 3.803 -1.4997 2.3882 0.7453
+ 56GLUT N 427 2.852 4.999 3.693 -0.9772 -0.0371 -0.6440
+ 56GLUT CA 428 2.766 5.105 3.639 -0.6244 0.3046 -0.5350
+ 56GLUT C 429 2.712 5.106 3.495 -0.6536 -1.7994 -0.5641
+ 56GLUT O 430 2.625 5.194 3.466 -2.0098 -3.1308 -0.6910
+ 56GLUT CB 431 2.875 5.206 3.620 -1.5745 0.9163 -3.1456
+ 56GLUT CG 432 2.973 5.192 3.509 2.0870 0.8395 -0.1300
+ 56GLUT CD 433 2.937 5.297 3.404 0.7246 -0.0781 -0.6239
+ 56GLUT OE1 434 2.851 5.374 3.452 1.1253 -0.5275 0.8912
+ 56GLUT OE2 435 3.044 5.347 3.369 0.4820 2.2158 1.5869
+ 56GLUT OXT 436 2.763 5.015 3.424 0.6892 -0.3818 -1.4774
+ 9.78680 9.78680 9.78680
diff --git a/user-doc/tutorials/lyon.txt b/user-doc/tutorials/lyon.txt
index 8df3e819d1455c27d623188983f19377054b4a82..7ccfc0f0c32611f3aae18f5e3baa13689c3ee851 100644
--- a/user-doc/tutorials/lyon.txt
+++ b/user-doc/tutorials/lyon.txt
@@ -225,7 +225,7 @@ gnuplot or some other plotting package. </b>
\hidden{Example time series}
\anchor lyon-time-series
-\image html lyon-time-series.png "Time series for the second and third moments of the distribution of coordination numbers for two trajectories of Lennard Jones 7. The time series on the left was computed from a trajectory that was performed at \f$k_B T = 0.2 \epsilon\f$, while the two time series on the right were computed at a temperature of \f$k_B T = 0.1 \epsilon\f$. You can see that at the higher temperature there are jumps between distinct minima in the energy landscape. At the lower temperature, however, the system remains trapped in a single basin in the energy lanscape"
+\image html lyon-time-series.png "Time series for the second and third moments of the distribution of coordination numbers for two trajectories of Lennard Jones 7. The time series on the left was computed from a trajectory that was performed at a temperature of 0.2, while the two time series on the right were computed at a temperature of 0.1. You can see that at the higher temperature there are jumps between distinct minima in the energy landscape. At the lower temperature, however, the system remains trapped in a single basin in the energy lanscape"
\endhidden
@@ -264,7 +264,7 @@ you are going to have to use many more time steps than you did in previous exerc
configuration space is explored at this lower temperature
\anchor lyon-lj7-fes
-\image html lyon-histograms-highT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at \f$k_B T = 0.2 \epsilon\f$ (left) and \f$k_B T = 0.1 \epsilon\f$."
+\image html lyon-histograms-highT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at a temperature of 0.2 (left) and at a temperature of 0.1."
\endhidden
@@ -278,7 +278,7 @@ in a lower temperature simulation. The fact that the histogram shows that the p
is not converged. The free energy will thus look like the one shown below instead of looking like the one in the previous hidden section:
\anchor lyon-lj7-fes2
-\image html lyon-histograms-lowT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at \f$k_B T = 0.2 \epsilon\f$ (left) and \f$k_B T = 0.1 \epsilon\f$."
+\image html lyon-histograms-lowT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at a temperature of 0.2 (left) and at a temperature of 0.1."
\endhidden
diff --git a/user-doc/tutorials/munster.txt b/user-doc/tutorials/munster.txt
index a5fc91061850f8a1f59b9227ab15078dba3b5aa7..bef53426ee78e2217490e478c780a080754f9e2a 100644
--- a/user-doc/tutorials/munster.txt
+++ b/user-doc/tutorials/munster.txt
@@ -248,7 +248,7 @@ the atomic positions. This is a very good way to understand what \ref WHOLEMOLEC
is actually doing. Try the following input
\plumedfile
-MOLINFO STRUCTURE=../TOPO/reference.pdb
+MOLINFO STRUCTURE=reference.pdb
DUMPATOMS FILE=test1.gro ATOMS=1-22
WHOLEMOLECULES ENTITY0=1-22
DUMPATOMS FILE=test2.gro ATOMS=1-22
@@ -279,15 +279,14 @@ psi: TORSION ATOMS=7,9,15,17
heavy: GROUP ATOMS=1,5,6,7,9,11,15,16,17,19
gyr: GYRATION ATOMS=heavy
PRINT ARG=phi,psi,gyr FILE=analyze
-HISTOGRAM ...
+myhist: HISTOGRAM ...
ARG=gyr
- USE_ALL_DATA
- KERNEL=discrete
+ KERNEL=DISCRETE
GRID_MIN=0
GRID_MAX=1
GRID_BIN=50
- GRID_WFILE=histogram
-... HISTOGRAM
+...
+DUMPGRID GRID=myhist FILE=histogram
\endplumedfile
An histogram with 50 bins will be performed on the gyration radius. Try to compute the histogram for
@@ -820,7 +819,7 @@ MOVINGRESTRAINT ...
LABEL=res
ARG=phi
STEP0=0 AT0=-0.5pi KAPPA0=5
- STEP1=10000 AT0=0.5pi
+ STEP1=10000 AT1=0.5pi
...
PRINT ARG=phi,psi,res.work,res.phi_cntr FILE=colvar
\endplumedfile