PLUMED-NEST

Project ID: plumID:20.033
Source: ANALYSIS/plumed_histogram.dat
Originally used with PLUMED version: 2.6
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

rmsd_closed: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVAR_final VALUESthe values to read from the file=rmsd_closed_charmm_6vxx IGNORE_TIME ignore the time in the colvar file
The READ action with label rmsd_closed calculates the following quantities:
 Quantity   
 Description  
rmsd_closed..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsrmsd_open: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=COLVAR_final VALUESthe values to read from the file=rmsd_open IGNORE_TIME ignore the time in the colvar file
The READ action with label rmsd_open calculates the following quantities:
 Quantity   
 Description  
rmsd_open..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=rmsd_closed,rmsd_open FILEthe name of the file on which to output these quantities=check

#rw: REWEIGHT_METAD TEMP=300
The PRINT action with label  calculates somethingHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=rmsd_closed,rmsd_open
  GRID_MIN the lower bounds for the grid=0,0
  GRID_MAX the upper bounds for the grid=2.0,2.0
  GRID_BINthe number of bins for the grid=200,200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.01,0.01
  #KERNEL=discrete
  #LOGWEIGHTS=rw
  LABELa label for the action so that its output can be referenced in the input to other actions=hh
... 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 obtainedDUMPGRIDOutput 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=hh FILE the file on which to write the grid=histo  STRIDE the frequency with which the grid should be output to the file=10000
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 LABELa label for the action so that its output can be referenced in the input to other actions=FES_temp TEMPthe temperature at which you are operating=300
The CONVERT_TO_FES action with label FES_temp calculates the following quantities:
 Quantity   
 Description  
FES_temp.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=FES_temp FILE the file on which to write the grid=fes_reweighted.dat STRIDE the frequency with which the grid should be output to the file=10000