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 GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=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 GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=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