PLUMED-NEST

Project ID: plumID:19.003
Source: EMMI-ClpP/PRODUCTION/plumed.dat
Originally used with PLUMED version: 2.6-dev
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

# read reference pdb file
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=ClpP_structure.pdb

# define heavy atoms group
Protein-H: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=Protein-H

# create emmi score
emmi: 
EMMI
Calculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details
 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
SIGMA_MIN
minimum uncertainty
=0.03 
TEMP
temperature
=300.0 
NL_STRIDE
The frequency with which we are updating the neighbor list
=100 
NL_CUTOFF
The cutoff in overlap for the neighbor list
=0.01 
NOISETYPE
functional form of the noise (GAUSS, OUTLIERS, MARGINAL)
=MARGINAL 
RESOLUTION
Cryo-EM map resolution
=0.1 
GMM_FILE
file with the parameters of the GMM components
=ClpP_GMM.dat 
ATOMS
atoms for which we calculate the density map, typically all heavy atoms
=Protein-H

# add as bias 
The EMMI action with label emmi calculates the following quantities:
 Quantity   
 Description  
emmi.scoreb
Bayesian score
emmi.acc
MC acceptance for uncertainty
emmi.sigma
uncertainty in the forward models and experiment
emmi.neff
effective number of replicasemr: 
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
=emmi.scoreb 
STRIDE
the frequency with which the forces due to the bias should be calculated
=4

# print useful stuff
The BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Description  
emr.bias
the instantaneous value of the bias potential
emr._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=emr 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=200 
FMT
the format that should be used to output real numbers
=%30.10f