PLUMED-NEST

Project ID: plumID:19.007
Source: EMMI-MT/plumed.dat
Originally used with PLUMED version: 2.6-dev
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# include topology info: this is needed to identify atom types
MOLINFO STRUCTURE=structure.pdb
# define all heavy atoms using GROMACS index file
# which can be created with gmx_mpi make_ndx
protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H
protein: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein
protein-no-negative: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-no-negative-no-h
# make protein whole: add reference position of first heavy atom (in nm)
WHOLEMOLECULES ADDREFERENCE ENTITY0=protein REF0=3.217,4.340,6.195
# create EMMI score
EMMI ...
LABEL=gmm NOPBC TEMP=300.0 NL_STRIDE=50 NL_CUTOFF=0.01
ATOMS=protein-no-negative GMM_FILE=AC_SYMM.dat
#ATOMS selects what is refined
# no-negative-no-h or no-h are reasonable
# resolution is not used - no Bfactor fitting
# SIGMA_MIN can go down to 0.02, must be > NL_CUTOFF,
# if crashes, raise back to 0.05,
# the larger the number the softer the contribution of the EM data
SIGMA_MIN=0.05 RESOLUTION=0.1 NOISETYPE=MARGINAL
...

# translate into bias
emr: BIASVALUE ARG=gmm.scoreb STRIDE=2
# print useful info to file
PRINT ARG=gmm.* FILE=COLVAR STRIDE=500