PLUMED-NEST

Project ID: plumID:20.015
Source: 2-EMMI/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

# uncomment next line if your restart
#RESTART

# load extra file
# set to correct location
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=EMMIVox.cpp

# include topology info - set path a PDB file
The LOAD action with label  calculates somethingMOLINFOThis 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=../0-TOPO/step5_charmm2gmx.pdb WHOLE The reference structure is whole, i

# define all heavy atoms - set path to index file
protein-h: 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)=../0-TOPO/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=PROT-H

# make protein whole and in the cell where map is defined
The GROUP action with label protein-h calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ...
ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file
EMST only for backward compatibility, as of PLUMED 2
ENTITY0the atoms that make up a molecule that you wish to align=1-6701
ENTITY1the atoms that make up a molecule that you wish to align=6702-6741
... WHOLEMOLECULES

# create EMMI score
EMMIVOXBayesian single-structure and ensemble refinement with cryo-EM maps. More details ...
# name of this action
LABELa label for the action so that its output can be referenced in the input to other actions=gmm
# general parameters - do not change this! 
TEMPtemperature=303.15 NL_STRIDEneighbor list update frequency=50 NL_CUTOFF=0.5 NS_CUTOFF=1.0
# define atoms for cryo-EM restraint and read experimental data
# set path to map file if not in current directory
ATOMSatoms used in the calculation of the density map, typically all heavy atoms=protein-h DATA_FILEfile with cryo-EM map=map_zoned_align.dat
# info about the experimental map
NORM_DENSITYintegral of experimental density=2068.185 RESOLUTIONcryo-EM map resolution=0.1 VOXEL=0.1012
# data likelihood (or noise model): Marginal
NOISETYPE=MARGINAL SIGMA_MINminimum density error=0.2
# write output
STATUS_FILEwrite a file with all the data useful for restart=EMMIStatus WRITE_STRIDEstride for writing status file=2500
...

# translate into bias - updated every 2 time steps
The EMMIVOX action with label gmm calculates the following quantities:
 Quantity   
 Description  
gmm.scoreb
Bayesian score
gmm.scale
scale factor
gmm.offset
offset
gmm.accB
Bfactor MC acceptance
gmm.kbt
temperature in energy unitemr: 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=gmm.scoreb STRIDEthe frequency with which the forces due to the bias should be calculated=2

# print output to file
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 filePRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=gmm.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=2500