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
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa 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: GROUPDefine 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_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

# 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: EMMICalculate 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_MINminimum uncertainty=0.03 TEMPtemperature=300.0 NL_STRIDEThe frequency with which we are updating the neighbor list=100 NL_CUTOFFThe cutoff in overlap for the neighbor list=0.01 NOISETYPEfunctional form of the noise (GAUSS, OUTLIERS, MARGINAL)=MARGINAL RESOLUTIONCryo-EM map resolution=0.1 GMM_FILEfile with the parameters of the GMM components=ClpP_GMM.dat ATOMSatoms 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: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=emmi.scoreb STRIDEthe frequency with which the forces due to the bias should be calculated=4

# print useful stuff
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=emr.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=200 FMTthe format that should be used to output real numbers=%30.10f