PLUMED-NEST

Project ID: plumID:19.068
Source: model/metad-model/plumed.dat
Originally used with PLUMED version: 2.7
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

p: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1

The POSITION action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the atom position
p.y
the y-component of the atom position
p.z
the z-component of the atom position
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
  
ARG
the input for this action is the scalar output from one or more other actions
=p.x
  
FILE
 a file in which the list of added hills is stored
=Hills.data
  
PACE
the frequency for hill addition
=500
  
HEIGHT
the heights of the Gaussian hills
=1
  
SIGMA
the widths of the Gaussian hills
=0.185815
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
  
INTERVAL
one dimensional lower and upper limits, outside the limits the system will not feel the biasing force
=-2.9,2.9
  
GRID_MIN
the lower bounds for the grid
=-3
  
GRID_MAX
the upper bounds for the grid
=3
  
GRID_BIN
the number of bins for the grid
=300
  
CALC_MAX_BIAS
 Set to TRUE if you want to compute the maximum of the metadynamics V(s, t)
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor $c(t)$
metad.maxbias
the maximum of the metadynamics V(s, t)
PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%g 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=Colvar.data 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y,metad.bias,metad.rct,metad.maxbias

ENDPLUMED
Terminate plumed input. More details


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