Aims
The aim of this tutorial is to introduce the users to the ISDB module and in particular to Metadynamics Metainference [23] [24] ensemble determination. We will reproduce the setup of the simulation for a simple system [86] . For a general overview of the problem of ensembles determination please read [25] .
Objectives
Once this tutorial is completed students will be able to:
- Setup their own PLUMED-ISDB simulation.
Resources
The TARBALL for this project contains the following files:
- charmm36-eef1sb.ff: the force-field files for gromacs (not needed)
- system: a folder with reference files for gromacs (not needed)
- reference-impl: a folder to perform a simple implicit solvent simulation
- reference-impl-pbmetad: a folder to perform a pbmetad implicit solvent simulation
- m_and_m: a folder to perform a metadynamics metainference simulation
Introduction
Molecular dynamics simulations are the ideal tool to determine at atomistic resolution the behavior of complex molecules. This great resolution power comes at the cost of approximations that affects the agreement with actual experimental observables. At the same time experimental data alone are generally speaking not enough to determine a structural ensemble due the inverse nature of the problem, that is to go from few observables to many atoms in many different configurations. Furthermore, experimental data are affected by errors of multiple nature, from noise, systematic errors and errors in their atomistic interpretation. Most important experimental data are the result of the averaging over the ensemble of structure so it is not trivial to deconvolve this signal. One possibility is that of employing MD simulations together with experimental data to generate simulations already corrected for the data themselves. With METAINFERENCE this is done on-the-fly by adding an additional energy to the system that takes into account the agreement with the experimental data considering the multiple sources of errors.
Run a reference simulation
The system we use is the EGAAWAASS peptide used in ref. [86] . First of all we will run a simulation in implicit solvent using the EEF1-SB CHARMM36 force field. EEF1-SB includes a correction to the standard backbone torsion potential of CHARMM36, an electrostatic interaction with a distance dependent dielectric constant and a simple gaussian form for the solvation energy. The first two terms are implemented in the force field and using table potentials while the latter is implemented as a collective variable in PLUMED, EEFSOLV .
Click on the labels of the actions for more information on what each action computes
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# this is optional and tell to VIM that this is a PLUMED file
# vim: ft=plumed
# see comments just below this input file
#SETTINGS MOLFILE=user-doc/tutorials/others/isdb-1/reference-impl/egaawaass.pdb
MOLINFO MOLTYPEcompulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible =protein STRUCTUREcompulsory keyword
a file in pdb format containing a reference structure. =egaawaass.pdb The MOLINFO action with label
WHOLEMOLECULES ENTITY0the atoms that make up a molecule that you wish to align. =1-111 The WHOLEMOLECULES action with label
# EEF1SB Implicit solvation
#SETTINGS AUXFILE=user-doc/tutorials/others/isdb-1/reference-impl/index.ndx
protein-h: GROUP NDX_FILEthe name of index file (gromacs syntax) =index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used
by default =Protein-H The GROUP action with label protein-h defines a group of atoms so that they can be referred to later in the input
solv: EEFSOLV ATOMSThe atoms to be included in the calculation, e.g. =protein-h NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
NL_STRIDEcompulsory keyword ( default=40 )
The frequency with which the neighbor list is updated. =20 NL_BUFFERcompulsory keyword ( default=0.1 )
The buffer to the intrinsic cutoff used when calculating pairwise interactions. =0.1 The EEFSOLV action with label solv calculates a single scalar value
bias: BIASVALUE ARG=solv
This can be run using gromacs (unfortunately recent versions of gromacs do not support Verlet groups with table potentials, so performances are currently sub-optimal on the gromacs side)
gmx_mpi mdrun -s run.tpr -table table.xvg -tablep table.xvg -plumed plumed-eef1.dat -v
In order to have a converged sampling for this reference ensemble calculation it is useful to setup a Metadynamics calculation. In particular we will use PBMETAD because it is then a natural choice for Metadynamics Metainference later.
Click on the labels of the actions for more information on what each action computes
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# this is optional and tell to VIM that this is a PLUMED file
# vim: ft=plumed
# see comments just below this input file
#SETTINGS MOLFILE=user-doc/tutorials/others/isdb-1/reference-impl/egaawaass.pdb
MOLINFO MOLTYPEcompulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible =protein STRUCTUREcompulsory keyword
a file in pdb format containing a reference structure. =egaawaass.pdb The MOLINFO action with label
WHOLEMOLECULES ENTITY0the atoms that make up a molecule that you wish to align. =1-111 The WHOLEMOLECULES action with label
# EEF1SB Implicit solvation
#SETTINGS AUXFILE=user-doc/tutorials/others/isdb-1/reference-impl/index.ndx
protein-h: GROUP NDX_FILEthe name of index file (gromacs syntax) =index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used
by default =Protein-H The GROUP action with label protein-h defines a group of atoms so that they can be referred to later in the input
solv: EEFSOLV ATOMSThe atoms to be included in the calculation, e.g. =protein-h NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
NL_STRIDEcompulsory keyword ( default=40 )
The frequency with which the neighbor list is updated. =20 NL_BUFFERcompulsory keyword ( default=0.1 )
The buffer to the intrinsic cutoff used when calculating pairwise interactions. =0.1 The EEFSOLV action with label solv calculates a single scalar value
bias: BIASVALUE ARGthe input for this action is the scalar output from one or more other actions. =solv The BIASVALUE action with label bias calculates the following quantities:
Quantity | Description |
bias.bias | the instantaneous value of the bias potential |
bias.solv_bias | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named solv |
# CVs, Psi9, Phi1 are not defined
psi1: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-1 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi1 calculates a single scalar value
psi2: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-2 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi2 calculates a single scalar value
psi3: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-3 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi3 calculates a single scalar value
psi4: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-4 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi4 calculates a single scalar value
psi5: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-5 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi5 calculates a single scalar value
psi6: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-6 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi6 calculates a single scalar value
psi7: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-7 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi7 calculates a single scalar value
psi8: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-8 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi8 calculates a single scalar value
phi2: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-2 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi2 calculates a single scalar value
phi3: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-3 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi3 calculates a single scalar value
phi4: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-4 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi4 calculates a single scalar value
phi5: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-5 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi5 calculates a single scalar value
phi6: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-6 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi6 calculates a single scalar value
phi7: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-7 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi7 calculates a single scalar value
phi8: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-8 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi8 calculates a single scalar value
phi9: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-9 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi9 calculates a single scalar value
ahc: ALPHARMSD RESIDUESthis command is used to specify the set of residues that could conceivably form part
of the secondary structure. =all TYPEcompulsory keyword ( default=DRMSD )
the manner in which RMSD alignment is performed. =OPTIMAL LESS_THANcalculate the number of variables less than a certain target value. ={RATIONAL R_0=0.12} The ALPHARMSD action with label ahc calculates a single scalar value
# Bulky Trp residue dihedral
dihtrp_cacb: TORSION ATOMSthe four atoms involved in the torsional angle =67,47,49,52 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label dihtrp_cacb calculates a single scalar value
dihtrp_cbcg: TORSION ATOMSthe four atoms involved in the torsional angle =47,49,52,53 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label dihtrp_cbcg calculates a single scalar value
protein-ca: GROUP NDX_FILEthe name of index file (gromacs syntax) =index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used
by default =C-alpha The GROUP action with label protein-ca defines a group of atoms so that they can be referred to later in the input
gyr: GYRATION TYPEcompulsory keyword ( default=RADIUS )
The type of calculation relative to the Gyration Tensor you want to perform =RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for. =protein-ca NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The GYRATION action with label gyr calculates a single scalar value
# PBMetaD
pb: PBMETAD ...
ARGthe input for this action is the scalar output from one or more other actions. =phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcg,ahc.lessthan
SIGMAcompulsory keyword
the widths of the Gaussian hills =0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.01
HEIGHTthe height of the Gaussian hills, one for all biases. =0.5
PACEcompulsory keyword
the frequency for hill addition, one for all biases =400
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases. =20
GRID_MINthe lower bounds for the grid =-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0
GRID_MAXthe upper bounds for the grid =pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,5
GRID_WSTRIDEfrequency for dumping the grid =5000
WALKERS_MPI( default=off ) Switch on MPI version of multiple walkers - not compatible with WALKERS_*
options other than WALKERS_DIR
...The PBMETAD action with label pb calculates a single scalar value
PRINT FILEthe name of the file on which to output these quantities =COLVAR ARGthe input for this action is the scalar output from one or more other actions. =phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcg,ahc.lessthan STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 The PRINT action with label
PRINT FILEthe name of the file on which to output these quantities =ENERGY ARGthe input for this action is the scalar output from one or more other actions. =bias.bias,pb.bias STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 The PRINT action with label
In this case we are running a multiple-replica simulation where the sampling is used to parallelize the Metadynamics time-dependent potential through the use of multiple walkers.
mpiexec -np 14 gmx_mpi mdrun -s topolnew -multi 14 -plumed plumed-eef1-pbmetad.dat -table table.xvg -tablep table.xvg >& log.out &
Metadynamics Metainference
The former simulations should provide a converged (check for this) ensemble for the peptide. As shown in [86] the agreement with the multiple available NMR experimental data is not perfect. In order to generate an ensemble compatible with most of the available experimental data it is possible to include them in the simulation using METAINFERENCE . To do so the forward models for the data sets should be defined in the input file. In this case we have backbone chemical shifts, CS2BACKBONE ; residual dipolar couplings for two bonds, RDC ; and J-couplings for multiple atoms, JCOUPLING. Once the forward models are defined for the data sets, the calculated data together with the corresponding experimental values can be used to calculate the metainference score. The metainference score is additive so it can be split into multiple METAINFERENCE entries. In this case we are using two metainference entries for the two sets of RDCs because these are compared with the experimental data modulo a constant that should be unique each data set. Then we use one metainference for all the jcouplings and another one for the chemical shifts.
Click on the labels of the actions for more information on what each action computes

# this is optional and tell to VIM that this is a PLUMED file
# vim: ft=plumed
# see comments just below this input file
#SETTINGS NREPLICAS=2
#SETTINGS MOLFILE=user-doc/tutorials/others/isdb-1/reference-impl/egaawaass.pdb
MOLINFO MOLTYPEcompulsory keyword ( default=protein )
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA
are compatible =protein STRUCTUREcompulsory keyword
a file in pdb format containing a reference structure. =egaawaass.pdb The MOLINFO action with label
WHOLEMOLECULES ENTITY0the atoms that make up a molecule that you wish to align. =1-111 The WHOLEMOLECULES action with label
# EEF1SB Implicit solvation
#SETTINGS AUXFILE=user-doc/tutorials/others/isdb-1/reference-impl/index.ndx
protein-h: GROUP NDX_FILEthe name of index file (gromacs syntax) =index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used
by default =Protein-H The GROUP action with label protein-h defines a group of atoms so that they can be referred to later in the input
solv: EEFSOLV ATOMSThe atoms to be included in the calculation, e.g. =protein-h NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
NL_STRIDEcompulsory keyword ( default=40 )
The frequency with which the neighbor list is updated. =20 NL_BUFFERcompulsory keyword ( default=0.1 )
The buffer to the intrinsic cutoff used when calculating pairwise interactions. =0.1 The EEFSOLV action with label solv calculates a single scalar value
bias: BIASVALUE ARGthe input for this action is the scalar output from one or more other actions. =solv The BIASVALUE action with label bias calculates the following quantities:
Quantity | Description |
bias.bias | the instantaneous value of the bias potential |
bias.solv_bias | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named solv |
# CVs, Psi9, Phi1 are not defined
psi1: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-1 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi1 calculates a single scalar value
psi2: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-2 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi2 calculates a single scalar value
psi3: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-3 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi3 calculates a single scalar value
psi4: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-4 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi4 calculates a single scalar value
psi5: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-5 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi5 calculates a single scalar value
psi6: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-6 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi6 calculates a single scalar value
psi7: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-7 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi7 calculates a single scalar value
psi8: TORSION ATOMSthe four atoms involved in the torsional angle =@psi-8 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label psi8 calculates a single scalar value
phi2: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-2 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi2 calculates a single scalar value
phi3: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-3 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi3 calculates a single scalar value
phi4: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-4 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi4 calculates a single scalar value
phi5: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-5 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi5 calculates a single scalar value
phi6: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-6 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi6 calculates a single scalar value
phi7: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-7 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi7 calculates a single scalar value
phi8: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-8 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi8 calculates a single scalar value
phi9: TORSION ATOMSthe four atoms involved in the torsional angle =@phi-9 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label phi9 calculates a single scalar value
ahc: ALPHARMSD RESIDUESthis command is used to specify the set of residues that could conceivably form part
of the secondary structure. =all TYPEcompulsory keyword ( default=DRMSD )
the manner in which RMSD alignment is performed. =OPTIMAL LESS_THANcalculate the number of variables less than a certain target value. ={RATIONAL R_0=0.12} The ALPHARMSD action with label ahc calculates a single scalar value
# Bulky Trp residue dihedral
dihtrp_cacb: TORSION ATOMSthe four atoms involved in the torsional angle =67,47,49,52 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label dihtrp_cacb calculates a single scalar value
dihtrp_cbcg: TORSION ATOMSthe four atoms involved in the torsional angle =47,49,52,53 NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The TORSION action with label dihtrp_cbcg calculates a single scalar value
protein-ca: GROUP NDX_FILEthe name of index file (gromacs syntax) =index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used
by default =C-alpha The GROUP action with label protein-ca defines a group of atoms so that they can be referred to later in the input
gyr: GYRATION TYPEcompulsory keyword ( default=RADIUS )
The type of calculation relative to the Gyration Tensor you want to perform =RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for. =protein-ca NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
The GYRATION action with label gyr calculates a single scalar value
# PBMetaD
pb: PBMETAD ...
ARGthe input for this action is the scalar output from one or more other actions. =phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcg,ahc.lessthan
SIGMAcompulsory keyword
the widths of the Gaussian hills =0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.1,0.01
HEIGHTthe height of the Gaussian hills, one for all biases. =0.5
PACEcompulsory keyword
the frequency for hill addition, one for all biases =400
BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases. =20
GRID_MINthe lower bounds for the grid =-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,0
GRID_MAXthe upper bounds for the grid =pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,5
GRID_WSTRIDEfrequency for dumping the grid =5000
WALKERS_MPI( default=off ) Switch on MPI version of multiple walkers - not compatible with WALKERS_*
options other than WALKERS_DIR
...The PBMETAD action with label pb calculates a single scalar value
PRINT FILEthe name of the file on which to output these quantities =COLVAR ARGthe input for this action is the scalar output from one or more other actions. =phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcg,ahc.lessthan STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 The PRINT action with label
PRINT FILEthe name of the file on which to output these quantities =ENERGY ARGthe input for this action is the scalar output from one or more other actions. =bias.bias,pb.bias STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 The PRINT action with label
# EXPERIMENTAL DATA SECTION
# RDCs (Grzesiek et al.)
# xGAAWAASS
nh: RDC ...
GYROMcompulsory keyword ( default=1. )
Add the product of the gyromagnetic constants for the bond. =-72.5388
SCALEcompulsory keyword ( default=1. )
Add the scaling factor to take into account concentration and other effects. =0.0001
NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
ATOMS1the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =18,19 COUPLING1Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-5.4
ATOMS2the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =25,26 COUPLING2Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-1.26
ATOMS3the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =35,36 COUPLING3Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-5.22
ATOMS4the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =45,46 COUPLING4Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-0.91
ATOMS5the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =69,70 COUPLING5Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=2.33
ATOMS6the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =79,80 COUPLING6Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-2.88
ATOMS7the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =89,90 COUPLING7Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-8.37
ATOMS8the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =100,101 COUPLING8Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-3.78
...The RDC action with label nh calculates the following quantities:
Quantity | Description |
nh.rdc-0 | the calculated # RDC This is the 0th of these quantities |
nh.rdc-1 | the calculated # RDC This is the 1th of these quantities |
nh.rdc-2 | the calculated # RDC This is the 2th of these quantities |
nh.rdc-3 | the calculated # RDC This is the 3th of these quantities |
nh.rdc-4 | the calculated # RDC This is the 4th of these quantities |
nh.rdc-5 | the calculated # RDC This is the 5th of these quantities |
nh.rdc-6 | the calculated # RDC This is the 6th of these quantities |
nh.rdc-7 | the calculated # RDC This is the 7th of these quantities |
nh.exp-0 | the experimental # RDC This is the 0th of these quantities |
nh.exp-1 | the experimental # RDC This is the 1th of these quantities |
nh.exp-2 | the experimental # RDC This is the 2th of these quantities |
nh.exp-3 | the experimental # RDC This is the 3th of these quantities |
nh.exp-4 | the experimental # RDC This is the 4th of these quantities |
nh.exp-5 | the experimental # RDC This is the 5th of these quantities |
nh.exp-6 | the experimental # RDC This is the 6th of these quantities |
nh.exp-7 | the experimental # RDC This is the 7th of these quantities |
# ExAAWAASx
caha: RDC ...
GYROMcompulsory keyword ( default=1. )
Add the product of the gyromagnetic constants for the bond. =179.9319
SCALEcompulsory keyword ( default=1. )
Add the scaling factor to take into account concentration and other effects. =0.0001
NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
ATOMS1the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =5,6 COUPLING1Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=12.95
ATOMS2the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =27,28 COUPLING2Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=11.5
ATOMS3the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =37,38 COUPLING3Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=21.42
ATOMS4the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =47,48 COUPLING4Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=-9.37
ATOMS5the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =71,72 COUPLING5Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=10.01
ATOMS6the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =81,82 COUPLING6Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=15.01
ATOMS7the couple of atoms involved in each of the bonds for which you wish to calculate
the RDC. =91,92 COUPLING7Add an experimental value for each coupling (needed by SVD and useful for \ref STATS)..
=15.73
...The RDC action with label caha calculates the following quantities:
Quantity | Description |
caha.rdc-0 | the calculated # RDC This is the 0th of these quantities |
caha.rdc-1 | the calculated # RDC This is the 1th of these quantities |
caha.rdc-2 | the calculated # RDC This is the 2th of these quantities |
caha.rdc-3 | the calculated # RDC This is the 3th of these quantities |
caha.rdc-4 | the calculated # RDC This is the 4th of these quantities |
caha.rdc-5 | the calculated # RDC This is the 5th of these quantities |
caha.rdc-6 | the calculated # RDC This is the 6th of these quantities |
caha.exp-0 | the experimental # RDC This is the 0th of these quantities |
caha.exp-1 | the experimental # RDC This is the 1th of these quantities |
caha.exp-2 | the experimental # RDC This is the 2th of these quantities |
caha.exp-3 | the experimental # RDC This is the 3th of these quantities |
caha.exp-4 | the experimental # RDC This is the 4th of these quantities |
caha.exp-5 | the experimental # RDC This is the 5th of these quantities |
caha.exp-6 | the experimental # RDC This is the 6th of these quantities |
#RDCS
byrdcnh: METAINFERENCE ...
ARGthe input for this action is the scalar output from one or more other actions. =(nh\.rdc-.*),pb.bias
PARARGreference values for the experimental data, these can be provided as arguments without
derivatives =(nh\.exp-.*)
REWEIGHT( default=off ) simple REWEIGHT using the latest ARG as energy
NOISETYPEcompulsory keyword ( default=MGAUSS )
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) =MGAUSS
OPTSIGMAMEANcompulsory keyword ( default=NONE )
Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly =SEM_MAX AVERAGINGStride for calculation of averaged weights and sigma_mean =400
SCALEDATA( default=off ) Set to TRUE if you want to sample a scaling factor common to all
values and replicas SCALE_PRIORcompulsory keyword ( default=FLAT )
either FLAT or GAUSSIAN =GAUSSIAN SCALE0 could not find this keyword =8.0 DSCALEmaximum MC move of the scaling factor =0.5
SIGMA0 could not find this keyword =5.0 SIGMA_MINcompulsory keyword ( default=0.0 )
minimum value of the uncertainty parameter =0.0001 SIGMA_MAXcompulsory keyword ( default=10. )
maximum value of the uncertainty parameter =15.0 DSIGMAmaximum MC move of the uncertainty parameter =0.1
WRITE_STRIDEcompulsory keyword ( default=10000 )
write the status to a file every N steps, this can be used for restart/continuation
=10000
...The METAINFERENCE action with label byrdcnh calculates the following quantities:
Quantity | Description |
byrdcnh.bias | the instantaneous value of the bias potential |
byrdcnh.biasDer | derivatives with respect to the bias |
byrdcnh.weight | weights of the weighted average |
byrdcnh.neff | effective number of replicas |
byrdcnh.scale | scale parameter |
byrdcnh.acceptScale | MC acceptance for scale value |
byrdcnh.acceptSigma | MC acceptance for sigma values |
byrdcnh.sigmaMean-0 | uncertainty in the mean estimate This is the 0th of these quantities |
byrdcnh.sigma-0 | uncertainty parameter This is the 0th of these quantities |
byrdcnh.sigmaMean-1 | uncertainty in the mean estimate This is the 1th of these quantities |
byrdcnh.sigma-1 | uncertainty parameter This is the 1th of these quantities |
byrdcnh.sigmaMean-2 | uncertainty in the mean estimate This is the 2th of these quantities |
byrdcnh.sigma-2 | uncertainty parameter This is the 2th of these quantities |
byrdcnh.sigmaMean-3 | uncertainty in the mean estimate This is the 3th of these quantities |
byrdcnh.sigma-3 | uncertainty parameter This is the 3th of these quantities |
byrdcnh.sigmaMean-4 | uncertainty in the mean estimate This is the 4th of these quantities |
byrdcnh.sigma-4 | uncertainty parameter This is the 4th of these quantities |
byrdcnh.sigmaMean-5 | uncertainty in the mean estimate This is the 5th of these quantities |
byrdcnh.sigma-5 | uncertainty parameter This is the 5th of these quantities |
byrdcnh.sigmaMean-6 | uncertainty in the mean estimate This is the 6th of these quantities |
byrdcnh.sigma-6 | uncertainty parameter This is the 6th of these quantities |
byrdcnh.sigmaMean-7 | uncertainty in the mean estimate This is the 7th of these quantities |
byrdcnh.sigma-7 | uncertainty parameter This is the 7th of these quantities |
#RDCS
byrdccaha: METAINFERENCE ...
ARGthe input for this action is the scalar output from one or more other actions. =(caha\.rdc-.*),pb.bias
PARARGreference values for the experimental data, these can be provided as arguments without
derivatives =(caha\.exp-.*)
REWEIGHT( default=off ) simple REWEIGHT using the latest ARG as energy
NOISETYPEcompulsory keyword ( default=MGAUSS )
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) =MGAUSS
OPTSIGMAMEANcompulsory keyword ( default=NONE )
Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly =SEM_MAX AVERAGINGStride for calculation of averaged weights and sigma_mean =400
SCALEDATA( default=off ) Set to TRUE if you want to sample a scaling factor common to all
values and replicas SCALE_PRIORcompulsory keyword ( default=FLAT )
either FLAT or GAUSSIAN =GAUSSIAN SCALE0 could not find this keyword =9.0 DSCALEmaximum MC move of the scaling factor =0.5
SIGMA0 could not find this keyword =5.0 SIGMA_MINcompulsory keyword ( default=0.0 )
minimum value of the uncertainty parameter =0.0001 SIGMA_MAXcompulsory keyword ( default=10. )
maximum value of the uncertainty parameter =15.0 DSIGMAmaximum MC move of the uncertainty parameter =0.1
WRITE_STRIDEcompulsory keyword ( default=10000 )
write the status to a file every N steps, this can be used for restart/continuation
=10000
...The METAINFERENCE action with label byrdccaha calculates the following quantities:
Quantity | Description |
byrdccaha.bias | the instantaneous value of the bias potential |
byrdccaha.biasDer | derivatives with respect to the bias |
byrdccaha.weight | weights of the weighted average |
byrdccaha.neff | effective number of replicas |
byrdccaha.scale | scale parameter |
byrdccaha.acceptScale | MC acceptance for scale value |
byrdccaha.acceptSigma | MC acceptance for sigma values |
byrdccaha.sigmaMean-0 | uncertainty in the mean estimate This is the 0th of these quantities |
byrdccaha.sigma-0 | uncertainty parameter This is the 0th of these quantities |
byrdccaha.sigmaMean-1 | uncertainty in the mean estimate This is the 1th of these quantities |
byrdccaha.sigma-1 | uncertainty parameter This is the 1th of these quantities |
byrdccaha.sigmaMean-2 | uncertainty in the mean estimate This is the 2th of these quantities |
byrdccaha.sigma-2 | uncertainty parameter This is the 2th of these quantities |
byrdccaha.sigmaMean-3 | uncertainty in the mean estimate This is the 3th of these quantities |
byrdccaha.sigma-3 | uncertainty parameter This is the 3th of these quantities |
byrdccaha.sigmaMean-4 | uncertainty in the mean estimate This is the 4th of these quantities |
byrdccaha.sigma-4 | uncertainty parameter This is the 4th of these quantities |
byrdccaha.sigmaMean-5 | uncertainty in the mean estimate This is the 5th of these quantities |
byrdccaha.sigma-5 | uncertainty parameter This is the 5th of these quantities |
byrdccaha.sigmaMean-6 | uncertainty in the mean estimate This is the 6th of these quantities |
byrdccaha.sigma-6 | uncertainty parameter This is the 6th of these quantities |
# xGxAWxASx
jhan: JCOUPLING ...
TYPEcompulsory keyword
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM) =HAN
NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-2 COUPLING1Add an experimental value for each coupling. =-0.49
ATOMS2the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-4 COUPLING2Add an experimental value for each coupling. =-0.54
ATOMS3the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-5 COUPLING3Add an experimental value for each coupling. =-0.53
ATOMS4the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-7 COUPLING4Add an experimental value for each coupling. =-0.39
ATOMS5the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@psi-8 COUPLING5Add an experimental value for each coupling. =-0.39
...The JCOUPLING action with label jhan calculates the following quantities:
Quantity | Description |
jhan.j-0 | the calculated J-coupling This is the 0th of these quantities |
jhan.j-1 | the calculated J-coupling This is the 1th of these quantities |
jhan.j-2 | the calculated J-coupling This is the 2th of these quantities |
jhan.j-3 | the calculated J-coupling This is the 3th of these quantities |
jhan.j-4 | the calculated J-coupling This is the 4th of these quantities |
jhan.exp-0 | the experimental J-coupling This is the 0th of these quantities |
jhan.exp-1 | the experimental J-coupling This is the 1th of these quantities |
jhan.exp-2 | the experimental J-coupling This is the 2th of these quantities |
jhan.exp-3 | the experimental J-coupling This is the 3th of these quantities |
jhan.exp-4 | the experimental J-coupling This is the 4th of these quantities |
# xxAAWAASS
jhahn: JCOUPLING ...
TYPEcompulsory keyword
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM) =HAHN
NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@phi-2 COUPLING1Add an experimental value for each coupling. =6.05
ATOMS2the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@phi-3 COUPLING2Add an experimental value for each coupling. =5.95
ATOMS3the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@phi-4 COUPLING3Add an experimental value for each coupling. =6.44
ATOMS4the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@phi-5 COUPLING4Add an experimental value for each coupling. =6.53
ATOMS5the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@phi-6 COUPLING5Add an experimental value for each coupling. =5.93
ATOMS6the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@phi-7 COUPLING6Add an experimental value for each coupling. =6.98
ATOMS7the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@phi-8 COUPLING7Add an experimental value for each coupling. =7.16
...The JCOUPLING action with label jhahn calculates the following quantities:
Quantity | Description |
jhahn.j-0 | the calculated J-coupling This is the 0th of these quantities |
jhahn.j-1 | the calculated J-coupling This is the 1th of these quantities |
jhahn.j-2 | the calculated J-coupling This is the 2th of these quantities |
jhahn.j-3 | the calculated J-coupling This is the 3th of these quantities |
jhahn.j-4 | the calculated J-coupling This is the 4th of these quantities |
jhahn.j-5 | the calculated J-coupling This is the 5th of these quantities |
jhahn.j-6 | the calculated J-coupling This is the 6th of these quantities |
jhahn.exp-0 | the experimental J-coupling This is the 0th of these quantities |
jhahn.exp-1 | the experimental J-coupling This is the 1th of these quantities |
jhahn.exp-2 | the experimental J-coupling This is the 2th of these quantities |
jhahn.exp-3 | the experimental J-coupling This is the 3th of these quantities |
jhahn.exp-4 | the experimental J-coupling This is the 4th of these quantities |
jhahn.exp-5 | the experimental J-coupling This is the 5th of these quantities |
jhahn.exp-6 | the experimental J-coupling This is the 6th of these quantities |
# xxxxWxxxx
jccg: JCOUPLING ...
TYPEcompulsory keyword
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM) =CCG
NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@chi1-5 COUPLING1Add an experimental value for each coupling. =1.59
...The JCOUPLING action with label jccg calculates the following quantities:
Quantity | Description |
jccg.j-0 | the calculated J-coupling This is the 0th of these quantities |
jccg.exp-0 | the experimental J-coupling This is the 0th of these quantities |
# xxxxWxxxx
jncg: JCOUPLING ...
TYPEcompulsory keyword
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM) =NCG
NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
ATOMS1the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling.
=@chi1-5 COUPLING1Add an experimental value for each coupling. =1.21
...The JCOUPLING action with label jncg calculates the following quantities:
Quantity | Description |
jncg.j-0 | the calculated J-coupling This is the 0th of these quantities |
jncg.exp-0 | the experimental J-coupling This is the 0th of these quantities |
#JC METAINFERENCE
byj: METAINFERENCE ...
ARGthe input for this action is the scalar output from one or more other actions. =(jhan\.j-.*),(jhahn\.j-.*),(jccg\.j.*),(jncg\.j.*),pb.bias
PARARGreference values for the experimental data, these can be provided as arguments without
derivatives =(jhan\.exp-.*),(jhahn\.exp-.*),(jccg\.exp.*),(jncg\.exp.*)
REWEIGHT( default=off ) simple REWEIGHT using the latest ARG as energy
NOISETYPEcompulsory keyword ( default=MGAUSS )
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) =MGAUSS
OPTSIGMAMEANcompulsory keyword ( default=NONE )
Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly =SEM_MAX AVERAGINGStride for calculation of averaged weights and sigma_mean =400
SIGMA0 could not find this keyword =5.0 SIGMA_MINcompulsory keyword ( default=0.0 )
minimum value of the uncertainty parameter =0.0001 SIGMA_MAXcompulsory keyword ( default=10. )
maximum value of the uncertainty parameter =15.0 DSIGMAmaximum MC move of the uncertainty parameter =0.1
WRITE_STRIDEcompulsory keyword ( default=10000 )
write the status to a file every N steps, this can be used for restart/continuation
=10000
...The METAINFERENCE action with label byj calculates the following quantities:
Quantity | Description |
byj.bias | the instantaneous value of the bias potential |
byj.biasDer | derivatives with respect to the bias |
byj.weight | weights of the weighted average |
byj.neff | effective number of replicas |
byj.acceptSigma | MC acceptance for sigma values |
byj.sigmaMean-0 | uncertainty in the mean estimate This is the 0th of these quantities |
byj.sigma-0 | uncertainty parameter This is the 0th of these quantities |
byj.sigmaMean-1 | uncertainty in the mean estimate This is the 1th of these quantities |
byj.sigma-1 | uncertainty parameter This is the 1th of these quantities |
byj.sigmaMean-2 | uncertainty in the mean estimate This is the 2th of these quantities |
byj.sigma-2 | uncertainty parameter This is the 2th of these quantities |
byj.sigmaMean-3 | uncertainty in the mean estimate This is the 3th of these quantities |
byj.sigma-3 | uncertainty parameter This is the 3th of these quantities |
byj.sigmaMean-4 | uncertainty in the mean estimate This is the 4th of these quantities |
byj.sigma-4 | uncertainty parameter This is the 4th of these quantities |
byj.sigmaMean-5 | uncertainty in the mean estimate This is the 5th of these quantities |
byj.sigma-5 | uncertainty parameter This is the 5th of these quantities |
byj.sigmaMean-6 | uncertainty in the mean estimate This is the 6th of these quantities |
byj.sigma-6 | uncertainty parameter This is the 6th of these quantities |
byj.sigmaMean-7 | uncertainty in the mean estimate This is the 7th of these quantities |
byj.sigma-7 | uncertainty parameter This is the 7th of these quantities |
byj.sigmaMean-8 | uncertainty in the mean estimate This is the 8th of these quantities |
byj.sigma-8 | uncertainty parameter This is the 8th of these quantities |
byj.sigmaMean-9 | uncertainty in the mean estimate This is the 9th of these quantities |
byj.sigma-9 | uncertainty parameter This is the 9th of these quantities |
byj.sigmaMean-10 | uncertainty in the mean estimate This is the 10th of these quantities |
byj.sigma-10 | uncertainty parameter This is the 10th of these quantities |
byj.sigmaMean-11 | uncertainty in the mean estimate This is the 11th of these quantities |
byj.sigma-11 | uncertainty parameter This is the 11th of these quantities |
byj.sigmaMean-12 | uncertainty in the mean estimate This is the 12th of these quantities |
byj.sigma-12 | uncertainty parameter This is the 12th of these quantities |
byj.sigmaMean-13 | uncertainty in the mean estimate This is the 13th of these quantities |
byj.sigma-13 | uncertainty parameter This is the 13th of these quantities |
# Chemical shifts
#SETTINGS AUXFOLDER=user-doc/tutorials/others/isdb-1/m_and_m/data
# Chemical shifts
cs: CS2BACKBONE ...
NOPBC( default=off ) ignore the periodic boundary conditions when calculating distances
ATOMSThe atoms to be included in the calculation, e.g. =1-111 DATADIRcompulsory keyword ( default=data/ )
The folder with the experimental chemical shifts. =data TEMPLATEcompulsory keyword ( default=template.pdb )
A PDB file of the protein system. =egaawaass.pdb DOSCORE( default=off ) activate metainference ARGthe input for this action is the scalar output from one or more other actions. =pb.bias
NOISETYPEcompulsory keyword ( default=MGAUSS )
functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC) =MGAUSS REWEIGHT( default=off ) simple REWEIGHT using the ARG as energy OPTSIGMAMEANcompulsory keyword ( default=NONE )
Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly =SEM_MAX AVERAGINGStride for calculation of averaged weights and sigma_mean =400
SIGMA0 could not find this keyword =4.0
SIGMA_MINcompulsory keyword ( default=0.0 )
minimum value of the uncertainty parameter =0.0001
SIGMA_MAXcompulsory keyword ( default=10. )
maximum value of the uncertainty parameter =5.00
WRITE_STRIDEcompulsory keyword ( default=10000 )
write the status to a file every N steps, this can be used for restart/continuation
=10000
...The CS2BACKBONE action with label cs calculates the following quantities:
Quantity | Description |
cs.ca-0-2 | the calculated Ca carbon chemical shifts This is the 0-2th of these quantities |
cs.ca-0-3 | the calculated Ca carbon chemical shifts This is the 0-3th of these quantities |
cs.ca-0-4 | the calculated Ca carbon chemical shifts This is the 0-4th of these quantities |
cs.ca-0-5 | the calculated Ca carbon chemical shifts This is the 0-5th of these quantities |
cs.ca-0-6 | the calculated Ca carbon chemical shifts This is the 0-6th of these quantities |
cs.ca-0-7 | the calculated Ca carbon chemical shifts This is the 0-7th of these quantities |
cs.ca-0-8 | the calculated Ca carbon chemical shifts This is the 0-8th of these quantities |
cs.cb-0-3 | the calculated Cb carbon chemical shifts This is the 0-3th of these quantities |
cs.cb-0-4 | the calculated Cb carbon chemical shifts This is the 0-4th of these quantities |
cs.cb-0-5 | the calculated Cb carbon chemical shifts This is the 0-5th of these quantities |
cs.cb-0-6 | the calculated Cb carbon chemical shifts This is the 0-6th of these quantities |
cs.cb-0-7 | the calculated Cb carbon chemical shifts This is the 0-7th of these quantities |
cs.cb-0-8 | the calculated Cb carbon chemical shifts This is the 0-8th of these quantities |
cs.co-0-2 | the calculated C' carbon chemical shifts This is the 0-2th of these quantities |
cs.co-0-3 | the calculated C' carbon chemical shifts This is the 0-3th of these quantities |
cs.co-0-4 | the calculated C' carbon chemical shifts This is the 0-4th of these quantities |
cs.co-0-5 | the calculated C' carbon chemical shifts This is the 0-5th of these quantities |
cs.co-0-6 | the calculated C' carbon chemical shifts This is the 0-6th of these quantities |
cs.co-0-7 | the calculated C' carbon chemical shifts This is the 0-7th of these quantities |
cs.co-0-8 | the calculated C' carbon chemical shifts This is the 0-8th of these quantities |
cs.ha-0-3 | the calculated Ha hydrogen chemical shifts This is the 0-3th of these quantities |
cs.ha-0-4 | the calculated Ha hydrogen chemical shifts This is the 0-4th of these quantities |
cs.ha-0-5 | the calculated Ha hydrogen chemical shifts This is the 0-5th of these quantities |
cs.ha-0-6 | the calculated Ha hydrogen chemical shifts This is the 0-6th of these quantities |
cs.ha-0-7 | the calculated Ha hydrogen chemical shifts This is the 0-7th of these quantities |
cs.ha-0-8 | the calculated Ha hydrogen chemical shifts This is the 0-8th of these quantities |
cs.hn-0-2 | the calculated H hydrogen chemical shifts This is the 0-2th of these quantities |
cs.hn-0-3 | the calculated H hydrogen chemical shifts This is the 0-3th of these quantities |
cs.hn-0-4 | the calculated H hydrogen chemical shifts This is the 0-4th of these quantities |
cs.hn-0-5 | the calculated H hydrogen chemical shifts This is the 0-5th of these quantities |
cs.hn-0-6 | the calculated H hydrogen chemical shifts This is the 0-6th of these quantities |
cs.hn-0-7 | the calculated H hydrogen chemical shifts This is the 0-7th of these quantities |
cs.hn-0-8 | the calculated H hydrogen chemical shifts This is the 0-8th of these quantities |
cs.nh-0-2 | the calculated N nitrogen chemical shifts This is the 0-2th of these quantities |
cs.nh-0-3 | the calculated N nitrogen chemical shifts This is the 0-3th of these quantities |
cs.nh-0-4 | the calculated N nitrogen chemical shifts This is the 0-4th of these quantities |
cs.nh-0-5 | the calculated N nitrogen chemical shifts This is the 0-5th of these quantities |
cs.nh-0-6 | the calculated N nitrogen chemical shifts This is the 0-6th of these quantities |
cs.nh-0-7 | the calculated N nitrogen chemical shifts This is the 0-7th of these quantities |
cs.nh-0-8 | the calculated N nitrogen chemical shifts This is the 0-8th of these quantities |
cs.score | the Metainference score |
cs.biasDer | derivatives with respect to the bias |
cs.weight | weights of the weighted average |
cs.neff | effective number of replicas |
cs.acceptSigma | MC acceptance for sigma values |
cs.sigmaMean-0 | uncertainty in the mean estimate This is the 0th of these quantities |
cs.sigma-0 | uncertainty parameter This is the 0th of these quantities |
cs.sigmaMean-1 | uncertainty in the mean estimate This is the 1th of these quantities |
cs.sigma-1 | uncertainty parameter This is the 1th of these quantities |
cs.sigmaMean-2 | uncertainty in the mean estimate This is the 2th of these quantities |
cs.sigma-2 | uncertainty parameter This is the 2th of these quantities |
cs.sigmaMean-3 | uncertainty in the mean estimate This is the 3th of these quantities |
cs.sigma-3 | uncertainty parameter This is the 3th of these quantities |
cs.sigmaMean-4 | uncertainty in the mean estimate This is the 4th of these quantities |
cs.sigma-4 | uncertainty parameter This is the 4th of these quantities |
cs.sigmaMean-5 | uncertainty in the mean estimate This is the 5th of these quantities |
cs.sigma-5 | uncertainty parameter This is the 5th of these quantities |
cs.sigmaMean-6 | uncertainty in the mean estimate This is the 6th of these quantities |
cs.sigma-6 | uncertainty parameter This is the 6th of these quantities |
cs.sigmaMean-7 | uncertainty in the mean estimate This is the 7th of these quantities |
cs.sigma-7 | uncertainty parameter This is the 7th of these quantities |
cs.sigmaMean-8 | uncertainty in the mean estimate This is the 8th of these quantities |
cs.sigma-8 | uncertainty parameter This is the 8th of these quantities |
cs.sigmaMean-9 | uncertainty in the mean estimate This is the 9th of these quantities |
cs.sigma-9 | uncertainty parameter This is the 9th of these quantities |
cs.sigmaMean-10 | uncertainty in the mean estimate This is the 10th of these quantities |
cs.sigma-10 | uncertainty parameter This is the 10th of these quantities |
cs.sigmaMean-11 | uncertainty in the mean estimate This is the 11th of these quantities |
cs.sigma-11 | uncertainty parameter This is the 11th of these quantities |
cs.sigmaMean-12 | uncertainty in the mean estimate This is the 12th of these quantities |
cs.sigma-12 | uncertainty parameter This is the 12th of these quantities |
cs.sigmaMean-13 | uncertainty in the mean estimate This is the 13th of these quantities |
cs.sigma-13 | uncertainty parameter This is the 13th of these quantities |
cs.sigmaMean-14 | uncertainty in the mean estimate This is the 14th of these quantities |
cs.sigma-14 | uncertainty parameter This is the 14th of these quantities |
cs.sigmaMean-15 | uncertainty in the mean estimate This is the 15th of these quantities |
cs.sigma-15 | uncertainty parameter This is the 15th of these quantities |
cs.sigmaMean-16 | uncertainty in the mean estimate This is the 16th of these quantities |
cs.sigma-16 | uncertainty parameter This is the 16th of these quantities |
cs.sigmaMean-17 | uncertainty in the mean estimate This is the 17th of these quantities |
cs.sigma-17 | uncertainty parameter This is the 17th of these quantities |
cs.sigmaMean-18 | uncertainty in the mean estimate This is the 18th of these quantities |
cs.sigma-18 | uncertainty parameter This is the 18th of these quantities |
cs.sigmaMean-19 | uncertainty in the mean estimate This is the 19th of these quantities |
cs.sigma-19 | uncertainty parameter This is the 19th of these quantities |
cs.sigmaMean-20 | uncertainty in the mean estimate This is the 20th of these quantities |
cs.sigma-20 | uncertainty parameter This is the 20th of these quantities |
cs.sigmaMean-21 | uncertainty in the mean estimate This is the 21th of these quantities |
cs.sigma-21 | uncertainty parameter This is the 21th of these quantities |
cs.sigmaMean-22 | uncertainty in the mean estimate This is the 22th of these quantities |
cs.sigma-22 | uncertainty parameter This is the 22th of these quantities |
cs.sigmaMean-23 | uncertainty in the mean estimate This is the 23th of these quantities |
cs.sigma-23 | uncertainty parameter This is the 23th of these quantities |
cs.sigmaMean-24 | uncertainty in the mean estimate This is the 24th of these quantities |
cs.sigma-24 | uncertainty parameter This is the 24th of these quantities |
cs.sigmaMean-25 | uncertainty in the mean estimate This is the 25th of these quantities |
cs.sigma-25 | uncertainty parameter This is the 25th of these quantities |
cs.sigmaMean-26 | uncertainty in the mean estimate This is the 26th of these quantities |
cs.sigma-26 | uncertainty parameter This is the 26th of these quantities |
cs.sigmaMean-27 | uncertainty in the mean estimate This is the 27th of these quantities |
cs.sigma-27 | uncertainty parameter This is the 27th of these quantities |
cs.sigmaMean-28 | uncertainty in the mean estimate This is the 28th of these quantities |
cs.sigma-28 | uncertainty parameter This is the 28th of these quantities |
cs.sigmaMean-29 | uncertainty in the mean estimate This is the 29th of these quantities |
cs.sigma-29 | uncertainty parameter This is the 29th of these quantities |
cs.sigmaMean-30 | uncertainty in the mean estimate This is the 30th of these quantities |
cs.sigma-30 | uncertainty parameter This is the 30th of these quantities |
cs.sigmaMean-31 | uncertainty in the mean estimate This is the 31th of these quantities |
cs.sigma-31 | uncertainty parameter This is the 31th of these quantities |
cs.sigmaMean-32 | uncertainty in the mean estimate This is the 32th of these quantities |
cs.sigma-32 | uncertainty parameter This is the 32th of these quantities |
cs.sigmaMean-33 | uncertainty in the mean estimate This is the 33th of these quantities |
cs.sigma-33 | uncertainty parameter This is the 33th of these quantities |
cs.sigmaMean-34 | uncertainty in the mean estimate This is the 34th of these quantities |
cs.sigma-34 | uncertainty parameter This is the 34th of these quantities |
cs.sigmaMean-35 | uncertainty in the mean estimate This is the 35th of these quantities |
cs.sigma-35 | uncertainty parameter This is the 35th of these quantities |
cs.sigmaMean-36 | uncertainty in the mean estimate This is the 36th of these quantities |
cs.sigma-36 | uncertainty parameter This is the 36th of these quantities |
cs.sigmaMean-37 | uncertainty in the mean estimate This is the 37th of these quantities |
cs.sigma-37 | uncertainty parameter This is the 37th of these quantities |
cs.sigmaMean-38 | uncertainty in the mean estimate This is the 38th of these quantities |
cs.sigma-38 | uncertainty parameter This is the 38th of these quantities |
cs.sigmaMean-39 | uncertainty in the mean estimate This is the 39th of these quantities |
cs.sigma-39 | uncertainty parameter This is the 39th of these quantities |
cs.expca-0-2 | the experimental Ca carbon chemical shifts This is the 0-2th of these quantities |
cs.expca-0-3 | the experimental Ca carbon chemical shifts This is the 0-3th of these quantities |
cs.expca-0-4 | the experimental Ca carbon chemical shifts This is the 0-4th of these quantities |
cs.expca-0-5 | the experimental Ca carbon chemical shifts This is the 0-5th of these quantities |
cs.expca-0-6 | the experimental Ca carbon chemical shifts This is the 0-6th of these quantities |
cs.expca-0-7 | the experimental Ca carbon chemical shifts This is the 0-7th of these quantities |
cs.expca-0-8 | the experimental Ca carbon chemical shifts This is the 0-8th of these quantities |
cs.expcb-0-3 | the experimental Cb carbon chemical shifts This is the 0-3th of these quantities |
cs.expcb-0-4 | the experimental Cb carbon chemical shifts This is the 0-4th of these quantities |
cs.expcb-0-5 | the experimental Cb carbon chemical shifts This is the 0-5th of these quantities |
cs.expcb-0-6 | the experimental Cb carbon chemical shifts This is the 0-6th of these quantities |
cs.expcb-0-7 | the experimental Cb carbon chemical shifts This is the 0-7th of these quantities |
cs.expcb-0-8 | the experimental Cb carbon chemical shifts This is the 0-8th of these quantities |
cs.expco-0-2 | the experimental C' carbon chemical shifts This is the 0-2th of these quantities |
cs.expco-0-3 | the experimental C' carbon chemical shifts This is the 0-3th of these quantities |
cs.expco-0-4 | the experimental C' carbon chemical shifts This is the 0-4th of these quantities |
cs.expco-0-5 | the experimental C' carbon chemical shifts This is the 0-5th of these quantities |
cs.expco-0-6 | the experimental C' carbon chemical shifts This is the 0-6th of these quantities |
cs.expco-0-7 | the experimental C' carbon chemical shifts This is the 0-7th of these quantities |
cs.expco-0-8 | the experimental C' carbon chemical shifts This is the 0-8th of these quantities |
cs.expha-0-3 | the experimental Ha hydrogen chemical shifts This is the 0-3th of these quantities |
cs.expha-0-4 | the experimental Ha hydrogen chemical shifts This is the 0-4th of these quantities |
cs.expha-0-5 | the experimental Ha hydrogen chemical shifts This is the 0-5th of these quantities |
cs.expha-0-6 | the experimental Ha hydrogen chemical shifts This is the 0-6th of these quantities |
cs.expha-0-7 | the experimental Ha hydrogen chemical shifts This is the 0-7th of these quantities |
cs.expha-0-8 | the experimental Ha hydrogen chemical shifts This is the 0-8th of these quantities |
cs.exphn-0-2 | the experimental H hydrogen chemical shifts This is the 0-2th of these quantities |
cs.exphn-0-3 | the experimental H hydrogen chemical shifts This is the 0-3th of these quantities |
cs.exphn-0-4 | the experimental H hydrogen chemical shifts This is the 0-4th of these quantities |
cs.exphn-0-5 | the experimental H hydrogen chemical shifts This is the 0-5th of these quantities |
cs.exphn-0-6 | the experimental H hydrogen chemical shifts This is the 0-6th of these quantities |
cs.exphn-0-7 | the experimental H hydrogen chemical shifts This is the 0-7th of these quantities |
cs.exphn-0-8 | the experimental H hydrogen chemical shifts This is the 0-8th of these quantities |
cs.expnh-0-2 | the experimental N nitrogen chemical shifts This is the 0-2th of these quantities |
cs.expnh-0-3 | the experimental N nitrogen chemical shifts This is the 0-3th of these quantities |
cs.expnh-0-4 | the experimental N nitrogen chemical shifts This is the 0-4th of these quantities |
cs.expnh-0-5 | the experimental N nitrogen chemical shifts This is the 0-5th of these quantities |
cs.expnh-0-6 | the experimental N nitrogen chemical shifts This is the 0-6th of these quantities |
cs.expnh-0-7 | the experimental N nitrogen chemical shifts This is the 0-7th of these quantities |
cs.expnh-0-8 | the experimental N nitrogen chemical shifts This is the 0-8th of these quantities |
mcs: BIASVALUE ARGthe input for this action is the scalar output from one or more other actions. =cs.score The BIASVALUE action with label mcs calculates the following quantities:
Quantity | Description |
mcs.bias | the instantaneous value of the bias potential |
mcs.cs.score_bias | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named cs.score |
# output from METAINFERENCE
PRINT ARGthe input for this action is the scalar output from one or more other actions. =byrdcnh.* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 FILEthe name of the file on which to output these quantities =BAYES.RDC.NH The PRINT action with label
PRINT ARGthe input for this action is the scalar output from one or more other actions. =byrdccaha.* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 FILEthe name of the file on which to output these quantities =BAYES.RDC.CAHA The PRINT action with label
PRINT ARGthe input for this action is the scalar output from one or more other actions. =byj.* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 FILEthe name of the file on which to output these quantities =BAYES.J The PRINT action with label
PRINT ARGthe input for this action is the scalar output from one or more other actions. =cs.* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =200 FILEthe name of the file on which to output these quantities =BAYES.CS The PRINT action with label
# the following are useful for the analysis on-the-fly of the quality of the agreement with the experimentl data
ens: ENSEMBLE ...
ARGthe input for this action is the scalar output from one or more other actions. =(nh\.rdc-.*),(caha\.rdc-.*),(jhan\.j-.*),(jhahn\.j-.*),(jccg\.j-.*),(jncg\.j-.*),(cs\...-.*),pb.bias REWEIGHT( default=off ) simple REWEIGHT using the latest ARG as energy
...The ENSEMBLE action with label ens calculates the following quantities:
Quantity | Description |
ens.nh.rdc-0 | the label of this action is set by user in the input. See documentation above. This is the 0th of these quantities |
ens.nh.rdc-1 | the label of this action is set by user in the input. See documentation above. This is the 1th of these quantities |
ens.nh.rdc-2 | the label of this action is set by user in the input. See documentation above. This is the 2th of these quantities |
ens.nh.rdc-3 | the label of this action is set by user in the input. See documentation above. This is the 3th of these quantities |
ens.nh.rdc-4 | the label of this action is set by user in the input. See documentation above. This is the 4th of these quantities |
ens.nh.rdc-5 | the label of this action is set by user in the input. See documentation above. This is the 5th of these quantities |
ens.nh.rdc-6 | the label of this action is set by user in the input. See documentation above. This is the 6th of these quantities |
ens.nh.rdc-7 | the label of this action is set by user in the input. See documentation above. This is the 7th of these quantities |
ens.caha.rdc-0 | the label of this action is set by user in the input. See documentation above. This is the 0th of these quantities |
ens.caha.rdc-1 | the label of this action is set by user in the input. See documentation above. This is the 1th of these quantities |
ens.caha.rdc-2 | the label of this action is set by user in the input. See documentation above. This is the 2th of these quantities |
ens.caha.rdc-3 | the label of this action is set by user in the input. See documentation above. This is the 3th of these quantities |
ens.caha.rdc-4 | the label of this action is set by user in the input. See documentation above. This is the 4th of these quantities |
ens.caha.rdc-5 | the label of this action is set by user in the input. See documentation above. This is the 5th of these quantities |
ens.caha.rdc-6 | the label of this action is set by user in the input. See documentation above. This is the 6th of these quantities |
ens.jhan.j-0 | the label of this action is set by user in the input. See documentation above. This is the 0th of these quantities |
ens.jhan.j-1 | the label of this action is set by user in the input. See documentation above. This is the 1th of these quantities |
ens.jhan.j-2 | the label of this action is set by user in the input. See documentation above. This is the 2th of these quantities |
ens.jhan.j-3 | the label of this action is set by user in the input. See documentation above. This is the 3th of these quantities |
ens.jhan.j-4 | the label of this action is set by user in the input. See documentation above. This is the 4th of these quantities |
ens.jhahn.j-0 | the label of this action is set by user in the input. See documentation above. This is the 0th of these quantities |
ens.jhahn.j-1 | the label of this action is set by user in the input. See documentation above. This is the 1th of these quantities |
ens.jhahn.j-2 | the label of this action is set by user in the input. See documentation above. This is the 2th of these quantities |
ens.jhahn.j-3 | the label of this action is set by user in the input. See documentation above. This is the 3th of these quantities |
ens.jhahn.j-4 | the label of this action is set by user in the input. See documentation above. This is the 4th of these quantities |
ens.jhahn.j-5 | the label of this action is set by user in the input. See documentation above. This is the 5th of these quantities |
ens.jhahn.j-6 | the label of this action is set by user in the input. See documentation above. This is the 6th of these quantities |
ens.jccg.j-0 | the label of this action is set by user in the input. See documentation above. This is the 0th of these quantities |
ens.jncg.j-0 | the label of this action is set by user in the input. See documentation above. This is the 0th of these quantities |
ens.cs.ca-0-2 | the label of this action is set by user in the input. See documentation above. This is the 0-2th of these quantities |
ens.cs.ca-0-3 | the label of this action is set by user in the input. See documentation above. This is the 0-3th of these quantities |
ens.cs.ca-0-4 | the label of this action is set by user in the input. See documentation above. This is the 0-4th of these quantities |
ens.cs.ca-0-5 | the label of this action is set by user in the input. See documentation above. This is the 0-5th of these quantities |
ens.cs.ca-0-6 | the label of this action is set by user in the input. See documentation above. This is the 0-6th of these quantities |
ens.cs.ca-0-7 | the label of this action is set by user in the input. See documentation above. This is the 0-7th of these quantities |
ens.cs.ca-0-8 | the label of this action is set by user in the input. See documentation above. This is the 0-8th of these quantities |
ens.cs.cb-0-3 | the label of this action is set by user in the input. See documentation above. This is the 0-3th of these quantities |
ens.cs.cb-0-4 | the label of this action is set by user in the input. See documentation above. This is the 0-4th of these quantities |
ens.cs.cb-0-5 | the label of this action is set by user in the input. See documentation above. This is the 0-5th of these quantities |
ens.cs.cb-0-6 | the label of this action is set by user in the input. See documentation above. This is the 0-6th of these quantities |
ens.cs.cb-0-7 | the label of this action is set by user in the input. See documentation above. This is the 0-7th of these quantities |
ens.cs.cb-0-8 | the label of this action is set by user in the input. See documentation above. This is the 0-8th of these quantities |
ens.cs.co-0-2 | the label of this action is set by user in the input. See documentation above. This is the 0-2th of these quantities |
ens.cs.co-0-3 | the label of this action is set by user in the input. See documentation above. This is the 0-3th of these quantities |
ens.cs.co-0-4 | the label of this action is set by user in the input. See documentation above. This is the 0-4th of these quantities |
ens.cs.co-0-5 | the label of this action is set by user in the input. See documentation above. This is the 0-5th of these quantities |
ens.cs.co-0-6 | the label of this action is set by user in the input. See documentation above. This is the 0-6th of these quantities |
ens.cs.co-0-7 | the label of this action is set by user in the input. See documentation above. This is the 0-7th of these quantities |
ens.cs.co-0-8 | the label of this action is set by user in the input. See documentation above. This is the 0-8th of these quantities |
ens.cs.ha-0-3 | the label of this action is set by user in the input. See documentation above. This is the 0-3th of these quantities |
ens.cs.ha-0-4 | the label of this action is set by user in the input. See documentation above. This is the 0-4th of these quantities |
ens.cs.ha-0-5 | the label of this action is set by user in the input. See documentation above. This is the 0-5th of these quantities |
ens.cs.ha-0-6 | the label of this action is set by user in the input. See documentation above. This is the 0-6th of these quantities |
ens.cs.ha-0-7 | the label of this action is set by user in the input. See documentation above. This is the 0-7th of these quantities |
ens.cs.ha-0-8 | the label of this action is set by user in the input. See documentation above. This is the 0-8th of these quantities |
ens.cs.hn-0-2 | the label of this action is set by user in the input. See documentation above. This is the 0-2th of these quantities |
ens.cs.hn-0-3 | the label of this action is set by user in the input. See documentation above. This is the 0-3th of these quantities |
ens.cs.hn-0-4 | the label of this action is set by user in the input. See documentation above. This is the 0-4th of these quantities |
ens.cs.hn-0-5 | the label of this action is set by user in the input. See documentation above. This is the 0-5th of these quantities |
ens.cs.hn-0-6 | the label of this action is set by user in the input. See documentation above. This is the 0-6th of these quantities |
ens.cs.hn-0-7 | the label of this action is set by user in the input. See documentation above. This is the 0-7th of these quantities |
ens.cs.hn-0-8 | the label of this action is set by user in the input. See documentation above. This is the 0-8th of these quantities |
ens.cs.nh-0-2 | the label of this action is set by user in the input. See documentation above. This is the 0-2th of these quantities |
ens.cs.nh-0-3 | the label of this action is set by user in the input. See documentation above. This is the 0-3th of these quantities |
ens.cs.nh-0-4 | the label of this action is set by user in the input. See documentation above. This is the 0-4th of these quantities |
ens.cs.nh-0-5 | the label of this action is set by user in the input. See documentation above. This is the 0-5th of these quantities |
ens.cs.nh-0-6 | the label of this action is set by user in the input. See documentation above. This is the 0-6th of these quantities |
ens.cs.nh-0-7 | the label of this action is set by user in the input. See documentation above. This is the 0-7th of these quantities |
ens.cs.nh-0-8 | the label of this action is set by user in the input. See documentation above. This is the 0-8th of these quantities |
nhst: STATS ...
ARGthe input for this action is the scalar output from one or more other actions. =(ens\.nh\.rdc-.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. =(nh\.exp-.*)
...The STATS action with label nhst calculates the following quantities:
Quantity | Description |
nhst.sqdevsum | the sum of the squared deviations between arguments and parameters |
nhst.corr | the correlation between arguments and parameters |
nhst.slope | the slope of a linear fit between arguments and parameters |
nhst.intercept | the intercept of a linear fit between arguments and parameters |
cahast: STATS ...
ARGthe input for this action is the scalar output from one or more other actions. =(ens\.caha\.rdc-.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. =(caha\.exp-.*)
...The STATS action with label cahast calculates the following quantities:
Quantity | Description |
cahast.sqdevsum | the sum of the squared deviations between arguments and parameters |
cahast.corr | the correlation between arguments and parameters |
cahast.slope | the slope of a linear fit between arguments and parameters |
cahast.intercept | the intercept of a linear fit between arguments and parameters |
csst: STATS ...
ARGthe input for this action is the scalar output from one or more other actions. =(ens\.cs\...-.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. =(cs\.exp.*)
...The STATS action with label csst calculates the following quantities:
Quantity | Description |
csst.sqdevsum | the sum of the squared deviations between arguments and parameters |
csst.corr | the correlation between arguments and parameters |
csst.slope | the slope of a linear fit between arguments and parameters |
csst.intercept | the intercept of a linear fit between arguments and parameters |
jhanst: STATS ...
ARGthe input for this action is the scalar output from one or more other actions. =(ens\.jhan\.j-.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. =(jhan\.exp-.*)
...The STATS action with label jhanst calculates the following quantities:
Quantity | Description |
jhanst.sqdevsum | the sum of the squared deviations between arguments and parameters |
jhanst.corr | the correlation between arguments and parameters |
jhanst.slope | the slope of a linear fit between arguments and parameters |
jhanst.intercept | the intercept of a linear fit between arguments and parameters |
jhahnst: STATS ...
ARGthe input for this action is the scalar output from one or more other actions. =(ens\.jhahn\.j-.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. =(jhahn\.exp-.*)
...The STATS action with label jhahnst calculates the following quantities:
Quantity | Description |
jhahnst.sqdevsum | the sum of the squared deviations between arguments and parameters |
jhahnst.corr | the correlation between arguments and parameters |
jhahnst.slope | the slope of a linear fit between arguments and parameters |
jhahnst.intercept | the intercept of a linear fit between arguments and parameters |
jw5ccyst: STATS ...
ARGthe input for this action is the scalar output from one or more other actions. =(ens\.jccg\.j.*),(ens\.jccg\.j.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. =(jccg\.exp-.*),(jccg\.exp-.*)
SQDEVSUM( default=off ) calculates only SQDEVSUM
...The STATS action with label jw5ccyst calculates a single scalar value
jw5ncyst: STATS ...
ARGthe input for this action is the scalar output from one or more other actions. =(ens\.jncg\.j.*),(ens\.jncg\.j.*) PARARGthe input for this action is the scalar output from one or more other actions without
derivatives. =(jncg\.exp-.*),(jncg\.exp-.*)
SQDEVSUM( default=off ) calculates only SQDEVSUM
...The STATS action with label jw5ncyst calculates a single scalar value
#output from STATS
PRINT ARGthe input for this action is the scalar output from one or more other actions. =nhst.* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =2000 FILEthe name of the file on which to output these quantities =ST.RDC.NH The PRINT action with label
PRINT ARGthe input for this action is the scalar output from one or more other actions. =cahast.* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =2000 FILEthe name of the file on which to output these quantities =ST.RDC.CAHA The PRINT action with label
PRINT ARGthe input for this action is the scalar output from one or more other actions. =csst.* STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =2000 FILEthe name of the file on which to output these quantities =ST.CS The PRINT action with label
PRINT ARG=jhanst.*,jhahnst.*,jw5ccyst.*,jw5ncyst.* STRIDE=2000 FILE=ST.J
As for the former case we are running a multiple-replica simulation where in addition to multiple-walker metadynamics we are also coupling the replicas through Metainference. The use of multiple-walkers metadynamics is here key in order to have the same bias defined for all the replicas. This allows us to calculate a weighted average of the experimental observables where the weights are defined univocally from the bias [24] .
mpiexec -np 14 gmx_mpi mdrun -s topolnew -multi 14 -plumed plumed-eef1-pbmetad-m_m.dat -table table.xvg -tablep table.xvg >& log.out &