Project ID: plumID:20.015
Source: EMMI-ASCT2/2-EMMI/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# uncomment next line if your restart
#RESTART

# load extra file
# set to correct location
LOAD FILE=EMMIVox.cpp

# include topology info - set path a PDB file
MOLINFO STRUCTURE=../0-TOPO/step5_charmm2gmx.pdb

# define all heavy atoms - set path to index file
protein-h: GROUP NDX_FILE=../0-TOPO/index.ndx NDX_GROUP=PROT-H

# make protein whole and in the cell where map is defined
WHOLEMOLECULES ...
ADDREFERENCE 
ENTITY0=1-6701         REF0=5.3607,4.5911,3.1497
ENTITY1=6702-6741      REF1=3.2439,3.3684,6.0308
... WHOLEMOLECULES

# create EMMI score
EMMIVOX ...
# name of this action
LABEL=gmm
# general parameters - do not change this! 
TEMP=303.15 NL_STRIDE=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
ATOMS=protein-h DATA_FILE=map_zoned_align.dat
# info about the experimental map
NORM_DENSITY=2068.185 RESOLUTION=0.1 VOXEL=0.1012
# data likelihood (or noise model): Marginal
NOISETYPE=MARGINAL SIGMA_MIN=0.2
# write output
STATUS_FILE=EMMIStatus WRITE_STRIDE=2500
...

# translate into bias - updated every 2 time steps
emr: BIASVALUE ARG=gmm.scoreb STRIDE=2

# print output to file
PRINT ARG=gmm.* FILE=COLVAR STRIDE=2500