PLUMED-NEST-TEST-SITE

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