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: 
READ
Read quantities from a colvar file. More details
 
FILE
the name of the file from which to read these quantities
=COLVAR_final 
VALUES
the 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 a scalar quantityrmsd_open: 
READ
Read quantities from a colvar file. More details
 
FILE
the name of the file from which to read these quantities
=COLVAR_final 
VALUES
the 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 a scalar quantity
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rmsd_closed,rmsd_open 
FILE
the name of the file on which to output these quantities
=check

#rw: REWEIGHT_METAD TEMP=300
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=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_BIN
the number of bins for the grid
=200,200
  
BANDWIDTH
the bandwidths for kernel density estimation
=0.01,0.01
  #KERNEL=discrete
  #LOGWEIGHTS=rw
  
LABEL
a 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 a scalar quantity
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the action that creates the grid you would like to output
=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_FES
Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x). More details
 
GRID
the action that creates the input grid you would like to use
=hh 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=FES_temp 
TEMP
the temperature at which you are operating
=300
The CONVERT_TO_FES action with label FES_temp calculates a scalar quantity
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the action that creates the grid you would like to output
=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