PLUMED-NEST-TEST-SITE

Project ID: plumID:21.018
Source: plumed_reweight/reweight_rho_hb.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

rho: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=../test_data/rtp_coord.dat VALUESthe values to read from the file=rho IGNORE_FORCES use this flag if the forces added by any bias can be safely ignored IGNORE_TIME ignore the time in the colvar file
The READ action with label rho calculates the following quantities:
 Quantity   
 Description  
rho..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailshb: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=../test_data/HB.dat VALUESthe values to read from the file=hb IGNORE_FORCES use this flag if the forces added by any bias can be safely ignored IGNORE_TIME ignore the time in the colvar file
The READ action with label hb calculates the following quantities:
 Quantity   
 Description  
hb..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsmetad: READRead quantities from a colvar file. More details FILEthe name of the file from which to read these quantities=../test_data/metad_data.dat VALUESthe values to read from the file=metad.* IGNORE_FORCES use this flag if the forces added by any bias can be safely ignored IGNORE_TIME ignore the time in the colvar file

The READ action with label metad calculates the following quantities:
 Quantity   
 Description  
metad..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsweights: REWEIGHT_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details TEMPthe system temperature=298 ARG the biases that must be taken into account when reweighting=metad.rbias

The REWEIGHT_METAD action with label weights calculates the following quantities:
 Quantity   
 Description  
weights.value
the weight to use for this frame to negate the effect the metadynamics biasHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=rho,hb
  GRID_MIN the lower bounds for the grid=0,0
  GRID_MAX the upper bounds for the grid=3.8,15
  GRID_BINthe number of bins for the grid=100,100
  KERNEL the kernel function you are using=GAUSSIAN
  BANDWIDTHthe bandwidths for kernel density esimtation=0.1,0.5
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=weights
  LABELa label for the action so that its output can be referenced in the input to other actions=hD
... HISTOGRAM

The HISTOGRAM action with label hD calculates the following quantities:
 Quantity   
 Description  
hD.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)=hD TEMPthe temperature at which you are operating=298
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=ff_output.dat


The DUMPGRID action with label  calculates somethingENDPLUMEDTerminate plumed input. More details