PLUMED-NEST

Project ID: plumID:19.050
Source: plumed_reweight.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 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
Activate restart. More details
# These two commands recompute the CV that was biased in the metadynamics calculation.
The RESTART action with label  calculates somethingcontThe 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 is used to calculate the final metadynamics bias.  This quantity is
 # required because it used when reweighting each of the trajectory frames.
 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 
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
   
PACE
the frequency for hill addition
=2000000000  # This is large so Gaussians are not added and the bias is constant.
   
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 
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
   
PACE
the frequency for hill addition
=2000000000  # This is large so Gaussians are not added and the bias is constant.
   
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
 ...
 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
 # 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.
cont2The DISTANCE_FROM_CONTOUR action with label cont2 calculates the following quantities:
 Quantity   
 Type   
 Description  
cont2.thickness
scalar
the distance between the two contours on the line from the reference atom
cont2.dist1
scalar
the distance between the reference atom and the nearest contour
cont2.dist2
scalar
the distance between the reference atom and the other contour
cont2.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
=1-2400 
ATOM
The atom whose perpendicular distance we are calculating from the contour
=2413  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.6,0.6,0.6  
DIR
the direction perpendicular to the contour that you are looking for
=z  
CONTOUR
the value we would like for the contour
=7.29
...
cont2: 
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
=1-2400 
ATOM
The atom whose perpendicular distance we are calculating from the contour
=2413  
BANDWIDTH
the bandwidths for kernel density esimtation
=0.6,0.6,0.6  
DIR
the direction perpendicular to the contour that you are looking for
=z  
CONTOUR
the value we would like for the contour
=7.29
 
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
...
 # When reweighting we must take both the MEAD and UPPER_WALLS into account
biasThe COMBINE action with label bias calculates the following quantities:
 Quantity   
 Type   
 Description  
bias
scalar
a linear compbination: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=*.bias 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=cont2.*,bias 
FILE
the name of the file on which to output these quantities
=COLVAR-reweight 
STRIDE
 the frequency with which the quantities of interest should be output
=1