PLUMED-NEST

Project ID: plumID:19.000
Source: model/plumed-metad.dat
Originally used with PLUMED version: 2.6-dev
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

ene: 
ENERGY
Calculate the total potential energy of the simulation box. More details
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
=1.2
  
SIGMA
the widths of the Gaussian hills
=0.35
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0
  
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
=100
  
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)$
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,ene

ENDPLUMED
Terminate plumed input. More details