PLUMED-NEST

Project ID: plumID:20.028
Source: wild-type/plumed-1.dat
Originally used with PLUMED version: 2.5
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

RESTART

FIT_TO_TEMPLATE REFERENCE=step5_charmm2gmx-modified-1.pdb
first: CENTER ATOMS=3006-3053       #  GTP
second: CENTER ATOMS=2955-3005      #  FAR
last: CENTER ATOMS=9733-33193:138   #  all P atoms in system--range with a stride 118
gtp: DISTANCE ATOMS=first,last COMPONENTS
far: DISTANCE ATOMS=second,last COMPONENTS

# Activate metadynamics in phi and psi
# depositing a Gaussian every 500 time steps,
# with height equal to 1.2 kJoule/mol,
# and width 0.35 rad for both CVs. 

METAD ...
LABEL=metad
ARG=gtp.z,far.z
PACE=500
HEIGHT=1.2
SIGMA=0.10,0.35
FILE=HILLS2
BIASFACTOR=5.0
TEMP=310.0
GRID_MIN=-15.0,-10.0
GRID_MAX=15.0,10.0
... METAD

# monitor the two variables and the metadynamics bias potential
PRINT STRIDE=200 ARG=gtp.z,far.z,metad.bias FILE=COLVAR2