Project ID: plumID:19.003
Source: EMMI-ClpP/PRODUCTION/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# read reference pdb file
MOLINFO STRUCTURE=ClpP_structure.pdb

# define heavy atoms group
Protein-H: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H

# create emmi score
emmi: EMMI NOPBC SIGMA_MIN=0.03 TEMP=300.0 NL_STRIDE=100 NL_CUTOFF=0.01 NOISETYPE=MARGINAL RESOLUTION=0.1 GMM_FILE=ClpP_GMM.dat ATOMS=Protein-H

# add as bias 
emr: BIASVALUE ARG=emmi.scoreb STRIDE=4

# print useful stuff
PRINT ARG=emr.* FILE=COLVAR STRIDE=200 FMT=%30.10f