PLUMED-NEST

Project ID: plumID:19.081
Source: Na/02_References/Example/Reweight/plumed.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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

refcv: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVARtrim VALUESthe values to read from the file=refcv.morethan IGNORE_TIME ignore the time in the colvar file
The READ action with label refcv calculates the following quantities:
 Quantity   
 Description  
refcv..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsb1: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVARtrim VALUESthe values to read from the file=b1.bias IGNORE_TIME ignore the time in the colvar file
The READ action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsuwall: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVARtrim VALUESthe values to read from the file=uwall.bias IGNORE_TIME ignore the time in the colvar file

The READ action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsbias: REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details TEMPthe system temperature=350.0 ARG the biases that must be taken into account when reweighting=b1.bias,uwall.bias

The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the biasHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=refcv.morethan
  GRID_MIN the lower bounds for the grid=-0.5
  GRID_MAX the upper bounds for the grid=250.5
  GRID_BINthe number of bins for the grid=1000
  BANDWIDTHthe bandwidths for kernel density esimtation=1.
  LABELa label for the action so that its output can be referenced in the input to other actions=hh
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
  STRIDE the frequency with which to store data for averaging=1
  CLEAR the frequency with whihc to clear the data that is being averaged=5000
... HISTOGRAM

The HISTOGRAM action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.value
the estimate of the histogram as a function of the argument that was obtainedff: CONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=hh TEMPthe temperature at which you are operating=350.0

The CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.value
the free energy surfaceDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDYou should use ARG instead of this keyword which was used in older versions of PLUMED and is provided for back compatibility only=ff FILE the file on which to write the grid=fes STRIDE the frequency with which the grid should be output to the file=5000

The DUMPGRID action with label  calculates somethingPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=1  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR