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
The MOLINFO action with label  calculates somethingProtein-HThe GROUP action with label Protein-H calculates the following quantities:
 Quantity   
 Type   
 Description  
Protein-H
atoms
indices of atoms specified in GROUP: 
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
emmiThe EMMI action with label emmi calculates the following quantities:
 Quantity   
 Type   
 Description  
emmi.scoreb
scalar
Bayesian score
emmi.neff
scalar
effective number of replicas: 
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 
emrThe BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Type   
 Description  
emr.bias
scalar
the instantaneous value of the bias potential
emr.emmi.scoreb_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 emmi.scoreb: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the labels of the scalar/vector arguments whose values will be used as a bias on the system
=emmi.scoreb 
STRIDE
the frequency with which the forces due to the bias should be calculated
=4

# print useful stuff
PRINT
Print quantities to a file. More details
 
ARG
the labels of the values that you would like to print to the file
=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