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

# The two lines below instruct PLUMED to calculate the distance between
# the adsorbate and the isosurface.  Notice how, as discussed in the main text,
# only a subset of the atoms in the membrane are used when we calculate the
# density as this reduces the computational expense.
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 instructs PLUMED to construct a metadynamics bias that is a
# function of the CV that is used in the main text.  In order to reduce the
# computational expense this bias is stored on a grid.  Furthermore, adaptive
# hills are used to ensure faster convergence of the final free energy surface
mm: METAD ...
  ARG=cont.qdist SIGMA=0.5 HEIGHT=1.3 PACE=100 BIASFACTOR=25 TEMP=325
  GRID_MIN=-15.0 GRID_MAX=100.0 GRID_BIN=115000
  ADAPTIVE=GEOM SIGMA_MIN=0.05 SIGMA_MAX=6.00
...
# This command instructs PLUMED to add a restraint that prevents the collective
# variable from taking high values. This restraint thus prevents the adsorbate
# from moving too far from the membrane surface.
uwall: UPPER_WALLS ARG=cont.qdist AT=50.0 KAPPA=1.0 EXP=2
# This command prints the value of the collective variable and the metadynamics
# bias to a file called colvar
PRINT ARG=cont.*,mm.* STRIDE=20 FILE=colvar