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=plumedEnables 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             #
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#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++#

UNITSThis command sets the internal units for the code. More details NATURAL use natural units

The UNITS action with label  calculates somethingpThe POSITION action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the atom position
p.y
scalar
the y-component of the atom position
p.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=1

ecvThe ECV_UMBRELLAS_LINE action with label ecv calculates the following quantities:
 Quantity   
 Type   
 Description  
ecv.p.x
scalar
the value of the argument named p.x: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action has hidden defaults. More details ...
  ARGthe labels of the scalar values that are input to this action=p.x
  CV_MINthe minimum of the CV range to be explored=-2.5
  CV_MAXthe maximum of the CV range to be explored=2.5
  SIGMAsigma of the umbrella Gaussians=0.185815
...
ecv: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action uses the defaults shown here. More details ...
  ARGthe labels of the scalar values that are input to this action=p.x
  CV_MINthe minimum of the CV range to be explored=-2.5
  CV_MAXthe maximum of the CV range to be explored=2.5
  SIGMAsigma of the umbrella Gaussians=0.185815
 TEMP temperature=-1 SPACING the distance between umbrellas, in units of SIGMA=1
...
opesThe OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details ARGthe 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 PACEhow often the bias is updated=500
opes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details ARGthe 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 PACEhow often the bias is updated=500  OBSERVATION_STEPS number of unbiased initial PACE steps to collect statistics for initialization=100 PRINT_STRIDE stride for printing to DELTAFS file, in units of PACE=100

PRINTPrint quantities to a file. More details FMTthe format that should be used to output real numbers=%g STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=Colvar.data ARGthe labels of the values that you would like to print to the file=p.x,p.y,opes.*

ENDPLUMEDTerminate 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