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

Click on the labels of the actions for more information on what each action computes
tested onv2.8
tested onmaster
# 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
Calculate functions of the density of atoms as a function of the box. This allows one to calculate More details
SPECIES
this keyword is used for colvars such as coordination number
=2-2400:12,10-2400:12
LOWMEM
lower the memory requirements
cont:
DISTANCE_FROM_CONTOUR
Calculate the perpendicular distance from a Willard-Chandler dividing surface. More details
...
DATA
The input base multicolvar which is being used to calculate the contour
=d1
ATOM
The atom whose perpendicular distance we are calculating from the contour
=2413
BANDWIDTH
the bandwidths for kernel density estimation
=3.0,3.0,3.0
DIR
the direction perpendicular to the contour that you are looking for
=z
CONTOUR
the value we would like for the 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
Used to performed metadynamics on one or more collective variables. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=cont.qdist
SIGMA
the widths of the Gaussian hills
=0.5
HEIGHT
the heights of the Gaussian hills
=1.3
PACE
the frequency for hill addition
=100
BIASFACTOR
use well tempered metadynamics and use this bias factor
=25
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=325
GRID_MIN
the lower bounds for the grid
=-15.0
GRID_MAX
the upper bounds for the grid
=100.0
GRID_BIN
the number of bins for the grid
=115000
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=GEOM
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.05
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=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
Defines a wall for the value of one or more collective variables, More details
ARG
the input for this action is the scalar output from one or more other actions
=cont.qdist
AT
the positions of the wall
=50.0
KAPPA
the force constant for the wall
=1.0
EXP
the powers for the walls
=2 # This command prints the value of the collective variable and the metadynamics # bias to a file called colvar
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=cont.*,mm
STRIDE
the frequency with which the quantities of interest should be output
=20
FILE
the name of the file on which to output these quantities
=colvar