Project ID: plumID:23.041
Source: 01-7p6a/2-Production/cc-0.8/plumed_EMMI.dat
Originally used with PLUMED version: 2.10
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
tested onv2.10
tested onmaster
# if you are restarting the run, please uncomment this line
#RESTART
# include topology info
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=../../1-Data/step3_input_xtc.pdb WHOLE The reference structure is whole, i
# define map atoms
system-map: 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)=../../1-Data/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=System-MAP
# define protein atoms
system-pro: 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)=../../1-Data/index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=System-PRO
# make protein whole
WHOLEMOLECULESThis 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=system-pro STRIDE the frequency with which molecules are reassembled=4
# Wrap water around protein
wrap-at: 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-wrap.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Wrap-ATOMS
wrap-ar: 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-wrap.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Wrap-AROUND
WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=wrap-at AROUNDreference atoms=wrap-ar PAIR Pair atoms in AROUND and ATOMS groups STRIDE the frequency with which molecules are reassembled=4

# 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=emmi
# general parameters - do not change this!
# NL_STRIDE: update neighbor list stride
# NL_DIST_CUTOFF: distance cutoff in nm
# NL_GAUSS_CUTOFF: cutoff based on the Gaussian sigma
TEMPtemperature=300.0 NL_STRIDEneighbor list update frequency=50 NL_DIST_CUTOFFneighbor list distance cutoff=1.0 NL_GAUSS_CUTOFFneighbor list Gaussian sigma cutoff=3.0
# define atoms for cryo-EM restraint and read experimental data
ATOMSatoms used in the calculation of the density map, typically all heavy atoms=system-map DATA_FILEfile with cryo-EM map=emd_plumed_aligned.dat
# info about the experimental map
NORM_DENSITYintegral of experimental density=687.556335 RESOLUTIONcryo-EM map resolution=0.19
# data likelihood (or noise model): Marginal
SIGMA_MINminimum density error=0.2 GPU calculate EMMIVOX on GPU with Libtorch
# output: in production write with the frequency at which XTC/TRR are written
STATUS_FILEwrite a file with all the data useful for restart=EMMIStatus WRITE_STRIDEstride for writing status file=5000
# comment this if you have a hetero-complex
BFACT_NOCHAIN Do not use chain ID for Bfactor MC
# in production, you should sample Bfactors
DBFACTBfactor MC step=0.05 MCBFACT_STRIDEBfactor MC stride=500 BFACT_SIGMABfactor sigma prior=0.1
# scale factor
SCALEscale factor=1.400000
# correlation
CORRELATION calculate correlation coefficient
...

# in production, apply bias to system
# translate into bias - updated every 2/4 time steps
# if simulation crashes, change to STRIDE=2
# IMPORTANT: in this case, update WHOLEMOLECULES and WRAPAROUND
# STRIDE parameters as well! 
# emr: BIASVALUE ARG=emmi.scoreb STRIDE=2
emr: 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
#
# include water positional restraint
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=../../1-Data/plumed_posres.dat
#
# print output to file
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=emmi.* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=5000