PLUMED-NEST

Project ID: plumID:19.025
Source: run-c22/plumed.dat
Originally used with PLUMED version: 2.4
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#SETTINGS NREPLICAS=2
# this is optional and tell to VIM that this is a PLUMED file
# vim: ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
# see comments just below this input file
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=template.pdb
The MOLINFO action with label  calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-111

# CVs, Psi9, Phi1 are not defined
psi1The TORSION action with label psi1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi1
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-1
the four atoms that are required to calculate the psi dihedral for residue 1. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
psi2The TORSION action with label psi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi2
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
psi3The TORSION action with label psi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi3
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-3
the four atoms that are required to calculate the psi dihedral for residue 3. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
psi4The TORSION action with label psi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi4
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
psi5The TORSION action with label psi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi5
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
psi6The TORSION action with label psi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi6
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-6
the four atoms that are required to calculate the psi dihedral for residue 6. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
psi7The TORSION action with label psi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi7
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
psi8The TORSION action with label psi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

phi2The TORSION action with label phi2 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi2
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
phi3The TORSION action with label phi3 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi3
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
phi4The TORSION action with label phi4 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi4
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
phi5The TORSION action with label phi5 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi5
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
phi6The TORSION action with label phi6 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi6
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
phi7The TORSION action with label phi7 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi7
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
phi8The TORSION action with label phi8 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi8
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
phi9The TORSION action with label phi9 calculates the following quantities:
 Quantity   
 Type   
 Description  
phi9
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=
@phi-9
the four atoms that are required to calculate the phi dihedral for residue 9. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# Bulky Trp residue dihedral
dihtrp_cacbThe TORSION action with label dihtrp_cacb calculates the following quantities:
 Quantity   
 Type   
 Description  
dihtrp_cacb
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=67,47,49,52
dihtrp_cbcgThe TORSION action with label dihtrp_cbcg calculates the following quantities:
 Quantity   
 Type   
 Description  
dihtrp_cbcg
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=47,49,52,53

gyrThe GYRATION action with label gyr calculates the following quantities:
 Quantity   
 Type   
 Description  
gyr
scalar
the radius of gyration: 
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=
@CA-1
the CA atom in residue 1. Click here for more information. 
,
@CA-2
the CA atom in residue 2. Click here for more information. 
,
@CA-3
the CA atom in residue 3. Click here for more information. 
,
@CA-4
the CA atom in residue 4. Click here for more information. 
,
@CA-5
the CA atom in residue 5. Click here for more information. 
,
@CA-6
the CA atom in residue 6. Click here for more information. 
,
@CA-7
the CA atom in residue 7. Click here for more information. 
,
@CA-8
the CA atom in residue 8. Click here for more information. 
,
@CA-9
the CA atom in residue 9. Click here for more information. 
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# PBMetaD
PBMETAD
Used to performed Parallel Bias metadynamics. More details
 ...
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pbThe PBMETAD action with label pb calculates the following quantities:
 Quantity   
 Type   
 Description  
pb.bias
scalar
the instantaneous value of the bias potential
    
ARG
the 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
    
SIGMA
the widths of the Gaussian hills
=1000 
    
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06,0.06
    
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6,0.6
    
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF
    
HEIGHT
the height of the Gaussian hills, one for all biases
=0.5
    
PACE
the frequency for hill addition, one for all biases
=200
    
BIASFACTOR
use well tempered metadynamics with this bias factor, one for all biases
=34
    
GRID_MIN
the lower bounds for the grid
=-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi,-pi
    
GRID_MAX
the upper bounds for the grid
=pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi,pi
    
GRID_WSTRIDE
frequency for dumping the grid
=50000
    
WALKERS_MPI
 Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
... PBMETAD

# output from the collective variable
PRINT
Print quantities to a file. More details
 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=gyr,phi2,phi3,phi4,phi5,phi6,phi7,phi8,phi9,psi1,psi2,psi3,psi4,psi5,psi6,psi7,psi8,dihtrp_cacb,dihtrp_cbcg 
STRIDE
 the frequency with which the quantities of interest should be output
=2000

# EXPERIMENTAL DATA SECTION

# RDCs (Grzesiek et al.)
# xGAAWAASS
RDC
Calculates the (Residual) Dipolar Coupling between two atoms. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
GYROM
 Add the product of the gyromagnetic constants for the bond
=-72.5388
    
SCALE
 Add the scaling factor to take into account concentration and other effects
=0.001
    
ATOMS1
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=18,19 
COUPLING1
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-5.4
    
ATOMS2
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=25,26 
COUPLING2
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-1.26
    
ATOMS3
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=35,36 
COUPLING3
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-5.22
    
ATOMS4
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=45,46 
COUPLING4
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-0.91
    
ATOMS5
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=69,70 
COUPLING5
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=2.33
    
ATOMS6
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=79,80 
COUPLING6
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-2.88
    
ATOMS7
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=89,90 
COUPLING7
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-8.37
    
ATOMS8
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=100,101 
COUPLING8
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-3.78
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=nhThe RDC action with label nh calculates the following quantities:
 Quantity   
 Type   
 Description  
nh.rdc-0
scalar
the calculated # RDC  This is the 0th of these quantities
nh.rdc-1
scalar
the calculated # RDC  This is the 1th of these quantities
nh.rdc-2
scalar
the calculated # RDC  This is the 2th of these quantities
nh.rdc-3
scalar
the calculated # RDC  This is the 3th of these quantities
nh.rdc-4
scalar
the calculated # RDC  This is the 4th of these quantities
nh.rdc-5
scalar
the calculated # RDC  This is the 5th of these quantities
nh.rdc-6
scalar
the calculated # RDC  This is the 6th of these quantities
nh.rdc-7
scalar
the calculated # RDC  This is the 7th of these quantities
nh.exp-0
scalar
the experimental # RDC  This is the 0th of these quantities
nh.exp-1
scalar
the experimental # RDC  This is the 1th of these quantities
nh.exp-2
scalar
the experimental # RDC  This is the 2th of these quantities
nh.exp-3
scalar
the experimental # RDC  This is the 3th of these quantities
nh.exp-4
scalar
the experimental # RDC  This is the 4th of these quantities
nh.exp-5
scalar
the experimental # RDC  This is the 5th of these quantities
nh.exp-6
scalar
the experimental # RDC  This is the 6th of these quantities
nh.exp-7
scalar
the experimental # RDC  This is the 7th of these quantities
nh.score
scalar
the Metainference score
nh.biasDer
scalar
derivatives with respect to the bias
nh.weight
scalar
weights of the weighted average
nh.neff
scalar
effective number of replicas
nh.scale
scalar
scale parameter
nh.acceptSigma
scalar
MC acceptance for sigma values
nh.sigmaMean-0
scalar
uncertainty in the mean estimate  This is the 0th of these quantities
nh.sigma-0
scalar
uncertainty parameter  This is the 0th of these quantities
nh.sigmaMean-1
scalar
uncertainty in the mean estimate  This is the 1th of these quantities
nh.sigma-1
scalar
uncertainty parameter  This is the 1th of these quantities
nh.sigmaMean-2
scalar
uncertainty in the mean estimate  This is the 2th of these quantities
nh.sigma-2
scalar
uncertainty parameter  This is the 2th of these quantities
nh.sigmaMean-3
scalar
uncertainty in the mean estimate  This is the 3th of these quantities
nh.sigma-3
scalar
uncertainty parameter  This is the 3th of these quantities
nh.sigmaMean-4
scalar
uncertainty in the mean estimate  This is the 4th of these quantities
nh.sigma-4
scalar
uncertainty parameter  This is the 4th of these quantities
nh.sigmaMean-5
scalar
uncertainty in the mean estimate  This is the 5th of these quantities
nh.sigma-5
scalar
uncertainty parameter  This is the 5th of these quantities
nh.sigmaMean-6
scalar
uncertainty in the mean estimate  This is the 6th of these quantities
nh.sigma-6
scalar
uncertainty parameter  This is the 6th of these quantities
nh.sigmaMean-7
scalar
uncertainty in the mean estimate  This is the 7th of these quantities
nh.sigma-7
scalar
uncertainty parameter  This is the 7th of these quantities
    
DOSCORE
 activate metainference
    
ARG
the input for this action is the scalar output from one or more other actions
=pb.bias
    
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200
    
REGRES_ZERO
stride for regression with zero offset
=200
    
SIGMA0
 initial value of the uncertainty parameter
=1.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=5.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1
    
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000
... RDC

mnhThe BIASVALUE action with label mnh calculates the following quantities:
 Quantity   
 Type   
 Description  
mnh.bias
scalar
the instantaneous value of the bias potential
mnh.nh.score_bias
scalar
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 nh.score: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nh.score 

# ExAAWAASx
RDC
Calculates the (Residual) Dipolar Coupling between two atoms. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
GYROM
 Add the product of the gyromagnetic constants for the bond
=179.9319
    
SCALE
 Add the scaling factor to take into account concentration and other effects
=0.001
    
ATOMS1
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=5,6 
COUPLING1
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=12.95
    
ATOMS2
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=27,28 
COUPLING2
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=11.5
    
ATOMS3
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=37,38 
COUPLING3
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=21.42
    
ATOMS4
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=47,48 
COUPLING4
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=-9.37
    
ATOMS5
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=71,72 
COUPLING5
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=10.01
    
ATOMS6
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=81,82 
COUPLING6
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=15.01
    
ATOMS7
the couple of atoms involved in each of the bonds for which you wish to calculate the RDC
=91,92 
COUPLING7
Add an experimental value for each coupling (needed by SVD and useful for STATS)
=15.73
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cahaThe RDC action with label caha calculates the following quantities:
 Quantity   
 Type   
 Description  
caha.rdc-0
scalar
the calculated # RDC  This is the 0th of these quantities
caha.rdc-1
scalar
the calculated # RDC  This is the 1th of these quantities
caha.rdc-2
scalar
the calculated # RDC  This is the 2th of these quantities
caha.rdc-3
scalar
the calculated # RDC  This is the 3th of these quantities
caha.rdc-4
scalar
the calculated # RDC  This is the 4th of these quantities
caha.rdc-5
scalar
the calculated # RDC  This is the 5th of these quantities
caha.rdc-6
scalar
the calculated # RDC  This is the 6th of these quantities
caha.exp-0
scalar
the experimental # RDC  This is the 0th of these quantities
caha.exp-1
scalar
the experimental # RDC  This is the 1th of these quantities
caha.exp-2
scalar
the experimental # RDC  This is the 2th of these quantities
caha.exp-3
scalar
the experimental # RDC  This is the 3th of these quantities
caha.exp-4
scalar
the experimental # RDC  This is the 4th of these quantities
caha.exp-5
scalar
the experimental # RDC  This is the 5th of these quantities
caha.exp-6
scalar
the experimental # RDC  This is the 6th of these quantities
caha.score
scalar
the Metainference score
caha.biasDer
scalar
derivatives with respect to the bias
caha.weight
scalar
weights of the weighted average
caha.neff
scalar
effective number of replicas
caha.scale
scalar
scale parameter
caha.acceptSigma
scalar
MC acceptance for sigma values
caha.sigmaMean-0
scalar
uncertainty in the mean estimate  This is the 0th of these quantities
caha.sigma-0
scalar
uncertainty parameter  This is the 0th of these quantities
caha.sigmaMean-1
scalar
uncertainty in the mean estimate  This is the 1th of these quantities
caha.sigma-1
scalar
uncertainty parameter  This is the 1th of these quantities
caha.sigmaMean-2
scalar
uncertainty in the mean estimate  This is the 2th of these quantities
caha.sigma-2
scalar
uncertainty parameter  This is the 2th of these quantities
caha.sigmaMean-3
scalar
uncertainty in the mean estimate  This is the 3th of these quantities
caha.sigma-3
scalar
uncertainty parameter  This is the 3th of these quantities
caha.sigmaMean-4
scalar
uncertainty in the mean estimate  This is the 4th of these quantities
caha.sigma-4
scalar
uncertainty parameter  This is the 4th of these quantities
caha.sigmaMean-5
scalar
uncertainty in the mean estimate  This is the 5th of these quantities
caha.sigma-5
scalar
uncertainty parameter  This is the 5th of these quantities
caha.sigmaMean-6
scalar
uncertainty in the mean estimate  This is the 6th of these quantities
caha.sigma-6
scalar
uncertainty parameter  This is the 6th of these quantities
    
DOSCORE
 activate metainference
    
ARG
the input for this action is the scalar output from one or more other actions
=pb.bias
    
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS  
REWEIGHT
 simple REWEIGHT using the ARG as energy
  
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200
    
REGRES_ZERO
stride for regression with zero offset
=200
    
SIGMA0
 initial value of the uncertainty parameter
=1.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=5.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1
    
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000
... RDC

mcahaThe BIASVALUE action with label mcaha calculates the following quantities:
 Quantity   
 Type   
 Description  
mcaha.bias
scalar
the instantaneous value of the bias potential
mcaha.caha.score_bias
scalar
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 caha.score: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=caha.score 

# xGxAWxASx
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=HAN
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=-0.49
    
ATOMS2
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
 
COUPLING2
Add an experimental value for each coupling
=-0.54
    
ATOMS3
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
 
COUPLING3
Add an experimental value for each coupling
=-0.53
    
ATOMS4
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
 
COUPLING4
Add an experimental value for each coupling
=-0.39
    
ATOMS5
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
 
COUPLING5
Add an experimental value for each coupling
=-0.39
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jhanThe JCOUPLING action with label jhan calculates the following quantities:
 Quantity   
 Type   
 Description  
jhan.j-0
scalar
the calculated J-coupling  This is the 0th of these quantities
jhan.j-1
scalar
the calculated J-coupling  This is the 1th of these quantities
jhan.j-2
scalar
the calculated J-coupling  This is the 2th of these quantities
jhan.j-3
scalar
the calculated J-coupling  This is the 3th of these quantities
jhan.j-4
scalar
the calculated J-coupling  This is the 4th of these quantities
jhan.exp-0
scalar
the experimental J-coupling  This is the 0th of these quantities
jhan.exp-1
scalar
the experimental J-coupling  This is the 1th of these quantities
jhan.exp-2
scalar
the experimental J-coupling  This is the 2th of these quantities
jhan.exp-3
scalar
the experimental J-coupling  This is the 3th of these quantities
jhan.exp-4
scalar
the experimental J-coupling  This is the 4th of these quantities
... JCOUPLING
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=HAN
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-2
the four atoms that are required to calculate the psi dihedral for residue 2. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=-0.49
    
ATOMS2
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-4
the four atoms that are required to calculate the psi dihedral for residue 4. Click here for more information. 
 
COUPLING2
Add an experimental value for each coupling
=-0.54
    
ATOMS3
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-5
the four atoms that are required to calculate the psi dihedral for residue 5. Click here for more information. 
 
COUPLING3
Add an experimental value for each coupling
=-0.53
    
ATOMS4
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-7
the four atoms that are required to calculate the psi dihedral for residue 7. Click here for more information. 
 
COUPLING4
Add an experimental value for each coupling
=-0.39
    
ATOMS5
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@psi-8
the four atoms that are required to calculate the psi dihedral for residue 8. Click here for more information. 
 
COUPLING5
Add an experimental value for each coupling
=-0.39
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jhan
 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=NONE 
SIGMA0
 initial value of the uncertainty parameter
=1.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10
... JCOUPLING

# xxAAWAASS
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=HAHN
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=6.05
    
ATOMS2
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
 
COUPLING2
Add an experimental value for each coupling
=5.95
    
ATOMS3
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
 
COUPLING3
Add an experimental value for each coupling
=6.44
    
ATOMS4
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
 
COUPLING4
Add an experimental value for each coupling
=6.53
    
ATOMS5
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
 
COUPLING5
Add an experimental value for each coupling
=5.93
    
ATOMS6
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
 
COUPLING6
Add an experimental value for each coupling
=6.98
    
ATOMS7
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
 
COUPLING7
Add an experimental value for each coupling
=7.16
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jhahnThe JCOUPLING action with label jhahn calculates the following quantities:
 Quantity   
 Type   
 Description  
jhahn.j-0
scalar
the calculated J-coupling  This is the 0th of these quantities
jhahn.j-1
scalar
the calculated J-coupling  This is the 1th of these quantities
jhahn.j-2
scalar
the calculated J-coupling  This is the 2th of these quantities
jhahn.j-3
scalar
the calculated J-coupling  This is the 3th of these quantities
jhahn.j-4
scalar
the calculated J-coupling  This is the 4th of these quantities
jhahn.j-5
scalar
the calculated J-coupling  This is the 5th of these quantities
jhahn.j-6
scalar
the calculated J-coupling  This is the 6th of these quantities
jhahn.exp-0
scalar
the experimental J-coupling  This is the 0th of these quantities
jhahn.exp-1
scalar
the experimental J-coupling  This is the 1th of these quantities
jhahn.exp-2
scalar
the experimental J-coupling  This is the 2th of these quantities
jhahn.exp-3
scalar
the experimental J-coupling  This is the 3th of these quantities
jhahn.exp-4
scalar
the experimental J-coupling  This is the 4th of these quantities
jhahn.exp-5
scalar
the experimental J-coupling  This is the 5th of these quantities
jhahn.exp-6
scalar
the experimental J-coupling  This is the 6th of these quantities
... JCOUPLING
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=HAHN
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-2
the four atoms that are required to calculate the phi dihedral for residue 2. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=6.05
    
ATOMS2
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-3
the four atoms that are required to calculate the phi dihedral for residue 3. Click here for more information. 
 
COUPLING2
Add an experimental value for each coupling
=5.95
    
ATOMS3
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-4
the four atoms that are required to calculate the phi dihedral for residue 4. Click here for more information. 
 
COUPLING3
Add an experimental value for each coupling
=6.44
    
ATOMS4
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-5
the four atoms that are required to calculate the phi dihedral for residue 5. Click here for more information. 
 
COUPLING4
Add an experimental value for each coupling
=6.53
    
ATOMS5
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-6
the four atoms that are required to calculate the phi dihedral for residue 6. Click here for more information. 
 
COUPLING5
Add an experimental value for each coupling
=5.93
    
ATOMS6
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-7
the four atoms that are required to calculate the phi dihedral for residue 7. Click here for more information. 
 
COUPLING6
Add an experimental value for each coupling
=6.98
    
ATOMS7
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@phi-8
the four atoms that are required to calculate the phi dihedral for residue 8. Click here for more information. 
 
COUPLING7
Add an experimental value for each coupling
=7.16
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jhahn
 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=NONE 
SIGMA0
 initial value of the uncertainty parameter
=1.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10
... JCOUPLING

# xxxxWxxxx
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=CCG
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@chi1-5
the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=1.59
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jccgThe JCOUPLING action with label jccg calculates the following quantities:
 Quantity   
 Type   
 Description  
jccg.j-0
scalar
the calculated J-coupling  This is the 0th of these quantities
jccg.exp-0
scalar
the experimental J-coupling  This is the 0th of these quantities
... JCOUPLING
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=CCG
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@chi1-5
the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=1.59
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jccg
 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=NONE 
SIGMA0
 initial value of the uncertainty parameter
=1.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10
... JCOUPLING

# xxxxWxxxx
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action has hidden defaults. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=NCG
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@chi1-5
the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=1.21
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jncgThe JCOUPLING action with label jncg calculates the following quantities:
 Quantity   
 Type   
 Description  
jncg.j-0
scalar
the calculated J-coupling  This is the 0th of these quantities
jncg.exp-0
scalar
the experimental J-coupling  This is the 0th of these quantities
... JCOUPLING
JCOUPLING
Calculates 3J coupling constants for a dihedral angle. This action uses the defaults shown here. More details
 ...
    
NOPBC
 ignore the periodic boundary conditions when calculating distances
    
TYPE
Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)
=NCG
    
ATOMS1
the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling
=
@chi1-5
the four atoms that are required to calculate the chi1 dihedral for residue 5. Click here for more information. 
 
COUPLING1
Add an experimental value for each coupling
=1.21
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=jncg
 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=NONE 
SIGMA0
 initial value of the uncertainty parameter
=1.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0 
SIGMA_MAX
 maximum value of the uncertainty parameter
=10
... JCOUPLING

METAINFERENCE
Calculates the Metainference energy for a set of experimental data. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=(jhan\.j-.*),(jhahn\.j-.*),(jccg\.j.*),(jncg\.j.*),pb.bias
    
PARARG
reference values for the experimental data, these can be provided as arguments without derivatives
=(jhan\.exp-.*),(jhahn\.exp-.*),(jccg\.exp.*),(jncg\.exp
    
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MGAUSS 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200
    
SIGMA0
 initial value of the uncertainty parameter
=2.5 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=5.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1
    
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=byjThe METAINFERENCE action with label byj calculates the following quantities:
 Quantity   
 Type   
 Description  
byj.bias
scalar
the instantaneous value of the bias potential
byj.biasDer
scalar
derivatives with respect to the bias
byj.weight
scalar
weights of the weighted average
byj.neff
scalar
effective number of replicas
byj.acceptSigma
scalar
MC acceptance for sigma values
byj.sigmaMean-0
scalar
uncertainty in the mean estimate  This is the 0th of these quantities
byj.sigma-0
scalar
uncertainty parameter  This is the 0th of these quantities
byj.sigmaMean-1
scalar
uncertainty in the mean estimate  This is the 1th of these quantities
byj.sigma-1
scalar
uncertainty parameter  This is the 1th of these quantities
byj.sigmaMean-2
scalar
uncertainty in the mean estimate  This is the 2th of these quantities
byj.sigma-2
scalar
uncertainty parameter  This is the 2th of these quantities
byj.sigmaMean-3
scalar
uncertainty in the mean estimate  This is the 3th of these quantities
byj.sigma-3
scalar
uncertainty parameter  This is the 3th of these quantities
byj.sigmaMean-4
scalar
uncertainty in the mean estimate  This is the 4th of these quantities
byj.sigma-4
scalar
uncertainty parameter  This is the 4th of these quantities
byj.sigmaMean-5
scalar
uncertainty in the mean estimate  This is the 5th of these quantities
byj.sigma-5
scalar
uncertainty parameter  This is the 5th of these quantities
byj.sigmaMean-6
scalar
uncertainty in the mean estimate  This is the 6th of these quantities
byj.sigma-6
scalar
uncertainty parameter  This is the 6th of these quantities
byj.sigmaMean-7
scalar
uncertainty in the mean estimate  This is the 7th of these quantities
byj.sigma-7
scalar
uncertainty parameter  This is the 7th of these quantities
byj.sigmaMean-8
scalar
uncertainty in the mean estimate  This is the 8th of these quantities
byj.sigma-8
scalar
uncertainty parameter  This is the 8th of these quantities
byj.sigmaMean-9
scalar
uncertainty in the mean estimate  This is the 9th of these quantities
byj.sigma-9
scalar
uncertainty parameter  This is the 9th of these quantities
byj.sigmaMean-10
scalar
uncertainty in the mean estimate  This is the 10th of these quantities
byj.sigma-10
scalar
uncertainty parameter  This is the 10th of these quantities
byj.sigmaMean-11
scalar
uncertainty in the mean estimate  This is the 11th of these quantities
byj.sigma-11
scalar
uncertainty parameter  This is the 11th of these quantities
byj.sigmaMean-12
scalar
uncertainty in the mean estimate  This is the 12th of these quantities
byj.sigma-12
scalar
uncertainty parameter  This is the 12th of these quantities
byj.sigmaMean-13
scalar
uncertainty in the mean estimate  This is the 13th of these quantities
byj.sigma-13
scalar
uncertainty parameter  This is the 13th of these quantities
... METAINFERENCE
#
# Chemical shifts
csThe CS2BACKBONE action with label cs calculates the following quantities:
 Quantity   
 Type   
 Description  
cs.ca-0-2
scalar
the calculated Ca carbon chemical shifts  This is the 0-2th of these quantities
cs.ca-0-3
scalar
the calculated Ca carbon chemical shifts  This is the 0-3th of these quantities
cs.ca-0-4
scalar
the calculated Ca carbon chemical shifts  This is the 0-4th of these quantities
cs.ca-0-5
scalar
the calculated Ca carbon chemical shifts  This is the 0-5th of these quantities
cs.ca-0-6
scalar
the calculated Ca carbon chemical shifts  This is the 0-6th of these quantities
cs.ca-0-7
scalar
the calculated Ca carbon chemical shifts  This is the 0-7th of these quantities
cs.ca-0-8
scalar
the calculated Ca carbon chemical shifts  This is the 0-8th of these quantities
cs.cb-0-3
scalar
the calculated Cb carbon chemical shifts  This is the 0-3th of these quantities
cs.cb-0-4
scalar
the calculated Cb carbon chemical shifts  This is the 0-4th of these quantities
cs.cb-0-5
scalar
the calculated Cb carbon chemical shifts  This is the 0-5th of these quantities
cs.cb-0-6
scalar
the calculated Cb carbon chemical shifts  This is the 0-6th of these quantities
cs.cb-0-7
scalar
the calculated Cb carbon chemical shifts  This is the 0-7th of these quantities
cs.cb-0-8
scalar
the calculated Cb carbon chemical shifts  This is the 0-8th of these quantities
cs.co-0-2
scalar
the calculated C' carbon chemical shifts  This is the 0-2th of these quantities
cs.co-0-3
scalar
the calculated C' carbon chemical shifts  This is the 0-3th of these quantities
cs.co-0-4
scalar
the calculated C' carbon chemical shifts  This is the 0-4th of these quantities
cs.co-0-5
scalar
the calculated C' carbon chemical shifts  This is the 0-5th of these quantities
cs.co-0-6
scalar
the calculated C' carbon chemical shifts  This is the 0-6th of these quantities
cs.co-0-7
scalar
the calculated C' carbon chemical shifts  This is the 0-7th of these quantities
cs.co-0-8
scalar
the calculated C' carbon chemical shifts  This is the 0-8th of these quantities
cs.ha-0-3
scalar
the calculated Ha hydrogen chemical shifts  This is the 0-3th of these quantities
cs.ha-0-4
scalar
the calculated Ha hydrogen chemical shifts  This is the 0-4th of these quantities
cs.ha-0-5
scalar
the calculated Ha hydrogen chemical shifts  This is the 0-5th of these quantities
cs.ha-0-6
scalar
the calculated Ha hydrogen chemical shifts  This is the 0-6th of these quantities
cs.ha-0-7
scalar
the calculated Ha hydrogen chemical shifts  This is the 0-7th of these quantities
cs.ha-0-8
scalar
the calculated Ha hydrogen chemical shifts  This is the 0-8th of these quantities
cs.hn-0-2
scalar
the calculated H hydrogen chemical shifts  This is the 0-2th of these quantities
cs.hn-0-3
scalar
the calculated H hydrogen chemical shifts  This is the 0-3th of these quantities
cs.hn-0-4
scalar
the calculated H hydrogen chemical shifts  This is the 0-4th of these quantities
cs.hn-0-5
scalar
the calculated H hydrogen chemical shifts  This is the 0-5th of these quantities
cs.hn-0-6
scalar
the calculated H hydrogen chemical shifts  This is the 0-6th of these quantities
cs.hn-0-7
scalar
the calculated H hydrogen chemical shifts  This is the 0-7th of these quantities
cs.hn-0-8
scalar
the calculated H hydrogen chemical shifts  This is the 0-8th of these quantities
cs.nh-0-2
scalar
the calculated N nitrogen chemical shifts  This is the 0-2th of these quantities
cs.nh-0-3
scalar
the calculated N nitrogen chemical shifts  This is the 0-3th of these quantities
cs.nh-0-4
scalar
the calculated N nitrogen chemical shifts  This is the 0-4th of these quantities
cs.nh-0-5
scalar
the calculated N nitrogen chemical shifts  This is the 0-5th of these quantities
cs.nh-0-6
scalar
the calculated N nitrogen chemical shifts  This is the 0-6th of these quantities
cs.nh-0-7
scalar
the calculated N nitrogen chemical shifts  This is the 0-7th of these quantities
cs.nh-0-8
scalar
the calculated N nitrogen chemical shifts  This is the 0-8th of these quantities
cs.score
scalar
the Metainference score
cs.biasDer
scalar
derivatives with respect to the bias
cs.weight
scalar
weights of the weighted average
cs.neff
scalar
effective number of replicas
cs.acceptSigma
scalar
MC acceptance for sigma values
cs.sigmaMean-0
scalar
uncertainty in the mean estimate  This is the 0th of these quantities
cs.sigma-0
scalar
uncertainty parameter  This is the 0th of these quantities
cs.sigmaMean-1
scalar
uncertainty in the mean estimate  This is the 1th of these quantities
cs.sigma-1
scalar
uncertainty parameter  This is the 1th of these quantities
cs.sigmaMean-2
scalar
uncertainty in the mean estimate  This is the 2th of these quantities
cs.sigma-2
scalar
uncertainty parameter  This is the 2th of these quantities
cs.sigmaMean-3
scalar
uncertainty in the mean estimate  This is the 3th of these quantities
cs.sigma-3
scalar
uncertainty parameter  This is the 3th of these quantities
cs.sigmaMean-4
scalar
uncertainty in the mean estimate  This is the 4th of these quantities
cs.sigma-4
scalar
uncertainty parameter  This is the 4th of these quantities
cs.sigmaMean-5
scalar
uncertainty in the mean estimate  This is the 5th of these quantities
cs.sigma-5
scalar
uncertainty parameter  This is the 5th of these quantities
cs.sigmaMean-6
scalar
uncertainty in the mean estimate  This is the 6th of these quantities
cs.sigma-6
scalar
uncertainty parameter  This is the 6th of these quantities
cs.sigmaMean-7
scalar
uncertainty in the mean estimate  This is the 7th of these quantities
cs.sigma-7
scalar
uncertainty parameter  This is the 7th of these quantities
cs.sigmaMean-8
scalar
uncertainty in the mean estimate  This is the 8th of these quantities
cs.sigma-8
scalar
uncertainty parameter  This is the 8th of these quantities
cs.sigmaMean-9
scalar
uncertainty in the mean estimate  This is the 9th of these quantities
cs.sigma-9
scalar
uncertainty parameter  This is the 9th of these quantities
cs.sigmaMean-10
scalar
uncertainty in the mean estimate  This is the 10th of these quantities
cs.sigma-10
scalar
uncertainty parameter  This is the 10th of these quantities
cs.sigmaMean-11
scalar
uncertainty in the mean estimate  This is the 11th of these quantities
cs.sigma-11
scalar
uncertainty parameter  This is the 11th of these quantities
cs.sigmaMean-12
scalar
uncertainty in the mean estimate  This is the 12th of these quantities
cs.sigma-12
scalar
uncertainty parameter  This is the 12th of these quantities
cs.sigmaMean-13
scalar
uncertainty in the mean estimate  This is the 13th of these quantities
cs.sigma-13
scalar
uncertainty parameter  This is the 13th of these quantities
cs.sigmaMean-14
scalar
uncertainty in the mean estimate  This is the 14th of these quantities
cs.sigma-14
scalar
uncertainty parameter  This is the 14th of these quantities
cs.sigmaMean-15
scalar
uncertainty in the mean estimate  This is the 15th of these quantities
cs.sigma-15
scalar
uncertainty parameter  This is the 15th of these quantities
cs.sigmaMean-16
scalar
uncertainty in the mean estimate  This is the 16th of these quantities
cs.sigma-16
scalar
uncertainty parameter  This is the 16th of these quantities
cs.sigmaMean-17
scalar
uncertainty in the mean estimate  This is the 17th of these quantities
cs.sigma-17
scalar
uncertainty parameter  This is the 17th of these quantities
cs.sigmaMean-18
scalar
uncertainty in the mean estimate  This is the 18th of these quantities
cs.sigma-18
scalar
uncertainty parameter  This is the 18th of these quantities
cs.sigmaMean-19
scalar
uncertainty in the mean estimate  This is the 19th of these quantities
cs.sigma-19
scalar
uncertainty parameter  This is the 19th of these quantities
cs.sigmaMean-20
scalar
uncertainty in the mean estimate  This is the 20th of these quantities
cs.sigma-20
scalar
uncertainty parameter  This is the 20th of these quantities
cs.sigmaMean-21
scalar
uncertainty in the mean estimate  This is the 21th of these quantities
cs.sigma-21
scalar
uncertainty parameter  This is the 21th of these quantities
cs.sigmaMean-22
scalar
uncertainty in the mean estimate  This is the 22th of these quantities
cs.sigma-22
scalar
uncertainty parameter  This is the 22th of these quantities
cs.sigmaMean-23
scalar
uncertainty in the mean estimate  This is the 23th of these quantities
cs.sigma-23
scalar
uncertainty parameter  This is the 23th of these quantities
cs.sigmaMean-24
scalar
uncertainty in the mean estimate  This is the 24th of these quantities
cs.sigma-24
scalar
uncertainty parameter  This is the 24th of these quantities
cs.sigmaMean-25
scalar
uncertainty in the mean estimate  This is the 25th of these quantities
cs.sigma-25
scalar
uncertainty parameter  This is the 25th of these quantities
cs.sigmaMean-26
scalar
uncertainty in the mean estimate  This is the 26th of these quantities
cs.sigma-26
scalar
uncertainty parameter  This is the 26th of these quantities
cs.sigmaMean-27
scalar
uncertainty in the mean estimate  This is the 27th of these quantities
cs.sigma-27
scalar
uncertainty parameter  This is the 27th of these quantities
cs.sigmaMean-28
scalar
uncertainty in the mean estimate  This is the 28th of these quantities
cs.sigma-28
scalar
uncertainty parameter  This is the 28th of these quantities
cs.sigmaMean-29
scalar
uncertainty in the mean estimate  This is the 29th of these quantities
cs.sigma-29
scalar
uncertainty parameter  This is the 29th of these quantities
cs.sigmaMean-30
scalar
uncertainty in the mean estimate  This is the 30th of these quantities
cs.sigma-30
scalar
uncertainty parameter  This is the 30th of these quantities
cs.sigmaMean-31
scalar
uncertainty in the mean estimate  This is the 31th of these quantities
cs.sigma-31
scalar
uncertainty parameter  This is the 31th of these quantities
cs.sigmaMean-32
scalar
uncertainty in the mean estimate  This is the 32th of these quantities
cs.sigma-32
scalar
uncertainty parameter  This is the 32th of these quantities
cs.sigmaMean-33
scalar
uncertainty in the mean estimate  This is the 33th of these quantities
cs.sigma-33
scalar
uncertainty parameter  This is the 33th of these quantities
cs.sigmaMean-34
scalar
uncertainty in the mean estimate  This is the 34th of these quantities
cs.sigma-34
scalar
uncertainty parameter  This is the 34th of these quantities
cs.sigmaMean-35
scalar
uncertainty in the mean estimate  This is the 35th of these quantities
cs.sigma-35
scalar
uncertainty parameter  This is the 35th of these quantities
cs.sigmaMean-36
scalar
uncertainty in the mean estimate  This is the 36th of these quantities
cs.sigma-36
scalar
uncertainty parameter  This is the 36th of these quantities
cs.sigmaMean-37
scalar
uncertainty in the mean estimate  This is the 37th of these quantities
cs.sigma-37
scalar
uncertainty parameter  This is the 37th of these quantities
cs.sigmaMean-38
scalar
uncertainty in the mean estimate  This is the 38th of these quantities
cs.sigma-38
scalar
uncertainty parameter  This is the 38th of these quantities
cs.sigmaMean-39
scalar
uncertainty in the mean estimate  This is the 39th of these quantities
cs.sigma-39
scalar
uncertainty parameter  This is the 39th of these quantities
cs.expca-0-2
scalar
the experimental Ca carbon chemical shifts  This is the 0-2th of these quantities
cs.expca-0-3
scalar
the experimental Ca carbon chemical shifts  This is the 0-3th of these quantities
cs.expca-0-4
scalar
the experimental Ca carbon chemical shifts  This is the 0-4th of these quantities
cs.expca-0-5
scalar
the experimental Ca carbon chemical shifts  This is the 0-5th of these quantities
cs.expca-0-6
scalar
the experimental Ca carbon chemical shifts  This is the 0-6th of these quantities
cs.expca-0-7
scalar
the experimental Ca carbon chemical shifts  This is the 0-7th of these quantities
cs.expca-0-8
scalar
the experimental Ca carbon chemical shifts  This is the 0-8th of these quantities
cs.expcb-0-3
scalar
the experimental Cb carbon chemical shifts  This is the 0-3th of these quantities
cs.expcb-0-4
scalar
the experimental Cb carbon chemical shifts  This is the 0-4th of these quantities
cs.expcb-0-5
scalar
the experimental Cb carbon chemical shifts  This is the 0-5th of these quantities
cs.expcb-0-6
scalar
the experimental Cb carbon chemical shifts  This is the 0-6th of these quantities
cs.expcb-0-7
scalar
the experimental Cb carbon chemical shifts  This is the 0-7th of these quantities
cs.expcb-0-8
scalar
the experimental Cb carbon chemical shifts  This is the 0-8th of these quantities
cs.expco-0-2
scalar
the experimental C' carbon chemical shifts  This is the 0-2th of these quantities
cs.expco-0-3
scalar
the experimental C' carbon chemical shifts  This is the 0-3th of these quantities
cs.expco-0-4
scalar
the experimental C' carbon chemical shifts  This is the 0-4th of these quantities
cs.expco-0-5
scalar
the experimental C' carbon chemical shifts  This is the 0-5th of these quantities
cs.expco-0-6
scalar
the experimental C' carbon chemical shifts  This is the 0-6th of these quantities
cs.expco-0-7
scalar
the experimental C' carbon chemical shifts  This is the 0-7th of these quantities
cs.expco-0-8
scalar
the experimental C' carbon chemical shifts  This is the 0-8th of these quantities
cs.expha-0-3
scalar
the experimental Ha hydrogen chemical shifts  This is the 0-3th of these quantities
cs.expha-0-4
scalar
the experimental Ha hydrogen chemical shifts  This is the 0-4th of these quantities
cs.expha-0-5
scalar
the experimental Ha hydrogen chemical shifts  This is the 0-5th of these quantities
cs.expha-0-6
scalar
the experimental Ha hydrogen chemical shifts  This is the 0-6th of these quantities
cs.expha-0-7
scalar
the experimental Ha hydrogen chemical shifts  This is the 0-7th of these quantities
cs.expha-0-8
scalar
the experimental Ha hydrogen chemical shifts  This is the 0-8th of these quantities
cs.exphn-0-2
scalar
the experimental H hydrogen chemical shifts  This is the 0-2th of these quantities
cs.exphn-0-3
scalar
the experimental H hydrogen chemical shifts  This is the 0-3th of these quantities
cs.exphn-0-4
scalar
the experimental H hydrogen chemical shifts  This is the 0-4th of these quantities
cs.exphn-0-5
scalar
the experimental H hydrogen chemical shifts  This is the 0-5th of these quantities
cs.exphn-0-6
scalar
the experimental H hydrogen chemical shifts  This is the 0-6th of these quantities
cs.exphn-0-7
scalar
the experimental H hydrogen chemical shifts  This is the 0-7th of these quantities
cs.exphn-0-8
scalar
the experimental H hydrogen chemical shifts  This is the 0-8th of these quantities
cs.expnh-0-2
scalar
the experimental N nitrogen chemical shifts  This is the 0-2th of these quantities
cs.expnh-0-3
scalar
the experimental N nitrogen chemical shifts  This is the 0-3th of these quantities
cs.expnh-0-4
scalar
the experimental N nitrogen chemical shifts  This is the 0-4th of these quantities
cs.expnh-0-5
scalar
the experimental N nitrogen chemical shifts  This is the 0-5th of these quantities
cs.expnh-0-6
scalar
the experimental N nitrogen chemical shifts  This is the 0-6th of these quantities
cs.expnh-0-7
scalar
the experimental N nitrogen chemical shifts  This is the 0-7th of these quantities
cs.expnh-0-8
scalar
the experimental N nitrogen chemical shifts  This is the 0-8th of these quantities: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. This action has hidden defaults. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
The atoms to be included in the calculation, e
=1-111 
DATADIR
 The folder with the experimental chemical shifts
=data 
TEMPLATE
 A PDB file of the protein system
=template.pdb 
DOSCORE
 activate metainference
 
ARG
the input for this action is the scalar output from one or more other actions
=pb.bias 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MOUTLIERS 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200 
SIGMA0
 initial value of the uncertainty parameter
=4.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=5.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000
cs: 
CS2BACKBONE
Calculates the backbone chemical shifts for a protein. This action uses the defaults shown here. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
ATOMS
The atoms to be included in the calculation, e
=1-111 
DATADIR
 The folder with the experimental chemical shifts
=data 
TEMPLATE
 A PDB file of the protein system
=template.pdb 
DOSCORE
 activate metainference
 
ARG
the input for this action is the scalar output from one or more other actions
=pb.bias 
NOISETYPE
 functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)
=MOUTLIERS 
REWEIGHT
 simple REWEIGHT using the ARG as energy
 
OPTSIGMAMEAN
 Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly
=SEM 
AVERAGING
Stride for calculation of averaged weights and sigma_mean
=200 
SIGMA0
 initial value of the uncertainty parameter
=4.0 
SIGMA_MIN
 minimum value of the uncertainty parameter
=0.0001 
SIGMA_MAX
 maximum value of the uncertainty parameter
=5.0 
DSIGMA
maximum MC move of the uncertainty parameter
=0.1 
WRITE_STRIDE
 write the status to a file every N steps, this can be used for restart/continuation
=10000  
NEIGH_FREQ
 Period in step for neighbor list update
=20
mcsThe BIASVALUE action with label mcs calculates the following quantities:
 Quantity   
 Type   
 Description  
mcs.bias
scalar
the instantaneous value of the bias potential
mcs.cs.score_bias
scalar
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: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cs.score

# output from METAINFERENCE
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=10000
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nh.score,nh.acceptSigma,nh.weight,nh.scale,(nh\.sigma   
STRIDE
 the frequency with which the quantities of interest should be output
=2000 
FILE
the name of the file on which to output these quantities
=BAYES.RDC.NH
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=caha.score,caha.acceptSigma,caha.weight,caha.scale,(caha\.sigma 
STRIDE
 the frequency with which the quantities of interest should be output
=2000 
FILE
the name of the file on which to output these quantities
=BAYES.RDC.CAHA
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=byj  
STRIDE
 the frequency with which the quantities of interest should be output
=2000 
FILE
the name of the file on which to output these quantities
=BAYES.J
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cs.score,cs.acceptSigma,cs.weight,(cs\.sigma   
STRIDE
 the frequency with which the quantities of interest should be output
=2000 
FILE
the name of the file on which to output these quantities
=BAYES.CS

# Calculate weighted ensemble average
ENSEMBLE
Calculates the replica averaging of a collective variable over multiple replicas. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=(nh\.rdc-.*),(caha\.rdc-.*),pb.bias 
REWEIGHT
 simple REWEIGHT using the latest ARG as energy
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ensThe ENSEMBLE action with label ens calculates the following quantities:
 Quantity   
 Type   
 Description  
ens.nh.rdc-0
scalar
the average for argument nh.rdc-0
ens.nh.rdc-1
scalar
the average for argument nh.rdc-1
ens.nh.rdc-2
scalar
the average for argument nh.rdc-2
ens.nh.rdc-3
scalar
the average for argument nh.rdc-3
ens.nh.rdc-4
scalar
the average for argument nh.rdc-4
ens.nh.rdc-5
scalar
the average for argument nh.rdc-5
ens.nh.rdc-6
scalar
the average for argument nh.rdc-6
ens.nh.rdc-7
scalar
the average for argument nh.rdc-7
ens.caha.rdc-0
scalar
the average for argument caha.rdc-0
ens.caha.rdc-1
scalar
the average for argument caha.rdc-1
ens.caha.rdc-2
scalar
the average for argument caha.rdc-2
ens.caha.rdc-3
scalar
the average for argument caha.rdc-3
ens.caha.rdc-4
scalar
the average for argument caha.rdc-4
ens.caha.rdc-5
scalar
the average for argument caha.rdc-5
ens.caha.rdc-6
scalar
the average for argument caha.rdc-6
... ENSEMBLE

# We use the analogous function for all other observables
STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=(ens\.nh\.rdc 
PARARG
the input for this action is the scalar output from one or more other actions without derivatives
=(nh\.exp
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=nhstThe STATS action with label nhst calculates the following quantities:
 Quantity   
 Type   
 Description  
nhst.sqdevsum
scalar
the sum of the squared deviations between arguments and parameters
nhst.corr
scalar
the correlation between arguments and parameters
nhst.slope
scalar
the slope of a linear fit between arguments and parameters
nhst.intercept
scalar
the intercept of a linear fit between arguments and parameters
... STATS

STATS
Calculates statistical properties of a set of collective variables with respect to a set of reference values. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=(ens\.caha\.rdc 
PARARG
the input for this action is the scalar output from one or more other actions without derivatives
=(caha\.exp
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cahastThe STATS action with label cahast calculates the following quantities:
 Quantity   
 Type   
 Description  
cahast.sqdevsum
scalar
the sum of the squared deviations between arguments and parameters
cahast.corr
scalar
the correlation between arguments and parameters
cahast.slope
scalar
the slope of a linear fit between arguments and parameters
cahast.intercept
scalar
the intercept of a linear fit between arguments and parameters
... STATS

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=nhst.*,cahast 
FILE
the name of the file on which to output these quantities
=STATS 
STRIDE
 the frequency with which the quantities of interest should be output
=2000

ENDPLUMED
Terminate plumed input. More details