PLUMED-NEST

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

# 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.
contThe DISTANCE_FROM_CONTOUR action with label cont calculates the following quantities:
 Quantity   
 Type   
 Description  
cont.thickness
scalar
the distance between the two contours on the line from the reference atom
cont.dist1
scalar
the distance between the reference atom and the nearest contour
cont.dist2
scalar
the distance between the reference atom and the other contour
cont.qdist
scalar
the differentiable (squared) distance between the two contours (see above): 
DISTANCE_FROM_CONTOUR
Calculate the perpendicular distance from a Willard-Chandler dividing surface. This action has hidden defaults. More details
 ...
  
POSITIONS
the positions of the atoms that we are calculating the contour from
=2-2400:12,10-2400:12 
ATOM
The atom whose perpendicular distance we are calculating from the contour
=2413 
BANDWIDTH
the bandwidths for kernel density esimtation
=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
...
cont: 
DISTANCE_FROM_CONTOUR
Calculate the perpendicular distance from a Willard-Chandler dividing surface. This action uses the defaults shown here. More details
 ...
  
POSITIONS
the positions of the atoms that we are calculating the contour from
=2-2400:12,10-2400:12 
ATOM
The atom whose perpendicular distance we are calculating from the contour
=2413 
BANDWIDTH
the bandwidths for kernel density esimtation
=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
 
KERNEL
 the kernel function you are using
=GAUSSIAN 
CUTOFF
 the cutoff at which to stop evaluating the kernel functions is set equal to sqrt(2*x)*bandwidth in each direction where x is this number
=6.25 
TOLERANCE
 this parameter is used to manage periodic boundary conditions
=0.1
...
# 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
mmThe METAD action with label mm calculates the following quantities:
 Quantity   
 Type   
 Description  
mm.bias
scalar
the instantaneous value of the bias potential: 
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. 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
...
mm: 
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. 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
 
FILE
 a file in which the list of added hills is stored
=HILLS
...
# 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.
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=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