PLUMED-NEST-TEST-SITE

Project ID: plumID:24.033
Source: Plumed-nest/7q4m/plumed_error.dat
Originally used with PLUMED version: 2.6
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

#RESTART
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=structure_noh.pdb

# define all heavy atoms using GROMACS index file
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)=noh_index.ndx  NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H

# make protein whole
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-638 ENTITY1the atoms that make up a molecule that you wish to align=639-1276 ENTITY2the atoms that make up a molecule that you wish to align=1277-1914 ENTITY3the atoms that make up a molecule that you wish to align=1915-2552 ENTITY4the atoms that make up a molecule that you wish to align=2553-3190 ENTITY5the atoms that make up a molecule that you wish to align=3191-3828 ENTITY6the atoms that make up a molecule that you wish to align=3829-4466 ENTITY7the atoms that make up a molecule that you wish to align=4467-5104 ENTITY8the atoms that make up a molecule that you wish to align=5105-5742 ENTITY9the atoms that make up a molecule that you wish to align=5743-6380 ENTITY10the atoms that make up a molecule that you wish to align=6381-7018 ENTITY11the atoms that make up a molecule that you wish to align=7019-7656 ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file

EMMICalculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=gmmThe EMMI action with label gmm calculates the following quantities:
 Quantity   
 Type   
 Description  
gmm.scoreb
scalar
Bayesian score
gmm.neff
scalar
effective number of replicas NOPBC ignore the periodic boundary conditions when calculating distances TEMPtemperature=310.0 NL_STRIDEThe frequency with which we are updating the neighbor list=1 NL_CUTOFFThe cutoff in overlap for the neighbor list=0.01
ATOMSatoms for which we calculate the density map, typically all heavy atoms=protein-h GMM_FILEfile with the parameters of the GMM components=map.dat
#the larger the number the softer the contribution of the EM data
SIGMA_MINminimum uncertainty=0.05 RESOLUTIONCryo-EM map resolution=0.25 NOISETYPEfunctional form of the noise (GAUSS, OUTLIERS, MARGINAL)=MARGINAL
#OPTSIGMAMEAN SIGMA_MEAN0=2.0
WRITE_OVwrite a file with model overlaps=OV_FILE.dat
WRITE_OV_STRIDEwrite model overlaps every N steps=1
NO_AVER don't do ensemble averaging in multi-replica mode
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=gmm.scoreb FILEthe name of the file on which to output these quantities=COLVAR_E STRIDE the frequency with which the quantities of interest should be output=1