PLUMED-NEST

Project ID: plumID:19.000
Source: model/plumed-ves.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. 
RESTART
Activate restart. 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
VES_DELTA_F
Implementation of VES Delta F method More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ves
  
ARG
the input for this action is the scalar output from one or more other actions
=p.x
  
TEMP
temperature is compulsory, but it can be sometimes fetched from the MD engine
=1
  
FILE_F0
names of files containing local free energies and derivatives
=fesA.data
  
FILE_F1
names of files containing local free energies and derivatives
=fesB.data
  
BIASFACTOR
 the gamma bias factor used for well-tempered target p(s)
=10.0
  
AV_STRIDE
 number of simulation steps between alpha updates
=500
  
M_STEP
 the mu step used for the Omega functional minimization
=0.05
  
PRINT_STRIDE
 stride for printing to ALPHA_FILE
=100
  
ALPHA_FILE
 file name for output minimization parameters
=Alpha.data
... VES_DELTA_F

The VES_DELTA_F action with label ves calculates the following quantities:
 Quantity   
 Description  
ves.bias
the instantaneous value of the bias potential
ves.rct
the reweighting factor c(t)
ves.work
the work done by the bias in one AV_STRIDE
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,ves.bias,ves.rct,ene

ENDPLUMED
Terminate plumed input. More details