Project ID: plumID:19.050
Source: plumed_reweight.dat
Originally used with PLUMED version: not specified
Stable: raw zipped stdout - stderr
Master: raw zipped stdout - stderr

# The consequence of including this command is that the bias values that are calculated
# by the METAD action are values for the final simulation bias.
RESTART
# These two commands recompute the CV that was biased in the metadynamics calculation.
d1: DENSITY SPECIES=2-2400:12,10-2400:12 LOWMEM
cont: DISTANCE_FROM_CONTOUR ...
   DATA=d1  ATOM=2413  BANDWIDTH=3.0,3.0,3.0  DIR=z  CONTOUR=0.42
...
 # This command is used to calculate the final metadynamics bias.  This quantity is
 # required because it used when reweighting each of the trajectory frames.
 mm: METAD ...
   ARG=cont.qdist SIGMA=0.5 HEIGHT=1.3 BIASFACTOR=25 TEMP=325
   PACE=2000000000  # This is large so Gaussians are not added and the bias is constant.
   GRID_MIN=-15.0 GRID_MAX=100.0 GRID_BIN=115000
   ADAPTIVE=GEOM SIGMA_MIN=0.05  SIGMA_MAX=6.00
 ...
 uwall: UPPER_WALLS ARG=cont.qdist AT=50.0 KAPPA=1.0 EXP=2
 # The two lines below instruct PLUMED to calculate the distance between the adsorbate and
 # the isosurface.  Notice, however, that, because we are now doing the analysis all of
 # the atoms in the membrane are used when we calculate the density.
d2: DENSITY SPECIES=1-2400
cont2: DISTANCE_FROM_CONTOUR ...
   DATA=d2  ATOM=2413  BANDWIDTH=0.6,0.6,0.6  DIR=z  CONTOUR=7.29
...
 # When reweighting we must take both the MEAD and UPPER_WALLS into account
bias: COMBINE ARG=*.bias PERIODIC=NO
PRINT ARG=cont2.*,bias FILE=COLVAR-reweight STRIDE=1