PLUMED-NEST

Project ID: plumID:20.022
Source: model/plumed.dat
Originally used with PLUMED version: 2.8
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. 

#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#
#                                                           #
#  This input generates a simulation that samples the same  #
#  distribution as 28 umbrella-sampling windows             #
#                                                           #
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#

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 positionecv: 
ECV_UMBRELLAS_LINE
Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=p.x
  
CV_MIN
the minimum of the CV range to be explored
=-2.5
  
CV_MAX
the maximum of the CV range to be explored
=2.5
  
SIGMA
sigma of the umbrella Gaussians
=0.185815
...
The ECV_UMBRELLAS_LINE action with label ecv calculates a scalar quantityopes: 
OPES_EXPANDED
On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details
 
ARG
the label of the ECVs that define the expansion
=ecv 
FILE
 a file with the estimate of the relative Delta F for each component of the target and of the global c(t)
=DeltaFs.data 
PACE
how often the bias is updated
=500

The OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
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,opes

ENDPLUMED
Terminate plumed input. More details


will produce 10 independent run, use instead WALKERS_MPI to make multiple walkers share bias

to print the running FES with GNUPLOT:
p '<awk ''END{for(i=3;i<=NF;i++)print -2.5+(i-3)*5/(NF-3),$i}'' DeltaFs.0.data'w lp