WHAM_HISTOGRAM

This is part of the analysis module

This can be used to output the a histogram using the weighted histogram technique

This shortcut action allows you to calculate a histogram using the weighted histogram analysis technique. For more detail on how this the weights for configurations are computed see REWEIGHT_WHAM

Examples

The following input can be used to analyze the output from a series of umbrella sampling calculations. The trajectory from each of the simulations run with the different biases should be concatenated into a single trajectory before running the following analysis script on the concatenated trajectory using PLUMED driver. The umbrella sampling simulations that will be analyzed using the script below applied a harmonic restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values. The script below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm to determine a weight for each configuration in the concatenated trajectory. A histogram is then constructed from the configurations visited and their weights. This histogram is then converted into a free energy surface and output to a file called fes.dat

Click on the labels of the actions for more information on what each action computes

contract shortcuts

#SETTINGS NREPLICAS=4
phi: TORSION ATOMSthe four atoms involved in the torsional angle =5,7,9,15 The TORSION action with label phi calculates a single scalar value
psi: TORSION ATOMSthe four atoms involved in the torsional angle =7,9,15,17 The TORSION action with label psi calculates a single scalar value
rp: RESTRAINT ARGthe input for this action is the scalar output from one or more other actions. =phi KAPPAcompulsory keyword ( default=0.0 )
specifies that the restraint is harmonic and what the values of the force constants
on each of the variables are =50.0 
   ATcompulsory keyword 
the position of the restraint =@replicas:{ 
         -3.00000000000000000000 
         -1.45161290322580645168 
         .09677419354838709664 
         1.64516129032258064496 
      }  
...The RESTRAINT action with label rp calculates the following quantities:

 Quantity   
 Description  
rp.bias
the instantaneous value of the bias potential
rp.force2
the instantaneous value of the squared force due to this bias potential


hh: WHAM_HISTOGRAM ARGcompulsory keyword 
the arguments that you would like to make the histogram for =phi BIAScompulsory keyword ( default=*.bias )
the value of the biases to use when performing WHAM =rp.bias TEMPcompulsory keyword 
the temperature at which the simulation was run =300 GRID_MINcompulsory keyword 
the minimum to use for the grid =-pi GRID_MAXcompulsory keyword 
the maximum to use for the grid =pi GRID_BINcompulsory keyword 
the number of bins to use for the grid =50 The WHAM_HISTOGRAM action with label hh
fes: CONVERT_TO_FES GRIDcompulsory keyword 
the action that creates the input grid you would like to use =hh TEMPthe temperature at which you are operating =300 The CONVERT_TO_FES action with label fes
DUMPGRID GRIDcompulsory keyword 
the action that creates the grid you would like to output =fes FILEcompulsory keyword ( default=density )
the file on which to write the grid. =fes.dat The DUMPGRID action with label 

#SETTINGS NREPLICAS=4
phi: TORSION ATOMSthe four atoms involved in the torsional angle =5,7,9,15 The TORSION action with label phi calculates a single scalar value
psi: TORSION ATOMSthe four atoms involved in the torsional angle =7,9,15,17 The TORSION action with label psi calculates a single scalar value
rp: RESTRAINT ARGthe input for this action is the scalar output from one or more other actions. =phi KAPPAcompulsory keyword ( default=0.0 )
specifies that the restraint is harmonic and what the values of the force constants
on each of the variables are =50.0 
   ATcompulsory keyword 
the position of the restraint =@replicas:{ 
         -3.00000000000000000000 
         -1.45161290322580645168 
         .09677419354838709664 
         1.64516129032258064496 
      }  
...The RESTRAINT action with label rp calculates the following quantities:

 Quantity   
 Description  
rp.bias
the instantaneous value of the bias potential
rp.force2
the instantaneous value of the squared force due to this bias potential


hh_weights: REWEIGHT_WHAM ARGcompulsory keyword ( default=*.bias )
the biases that must be taken into account when reweighting =rp.bias TEMPthe system temperature. =300 The REWEIGHT_WHAM action with label hh_weights calculates a single scalar value
hh_collect: COLLECT_FRAMES LOGWEIGHTSlist of actions that calculates log weights that should be used to weight configurations
when calculating averages =hh_weights STRIDEthe frequency with which data should be stored for analysis. =1 ARGthe input for this action is the scalar output from one or more other actions. =phi The COLLECT_FRAMES action with label hh_collect calculates a single scalar value
hh: HISTOGRAM ARGthe input for this action is the scalar output from one or more other actions. =hh_collect.* GRID_MINcompulsory keyword 
the lower bounds for the grid =-pi GRID_MAXcompulsory keyword 
the upper bounds for the grid =pi GRID_BINthe number of bins for the grid =50 KERNELcompulsory keyword ( default=gaussian )
the kernel function you are using. =DISCRETE The HISTOGRAM action with label hh
fes: CONVERT_TO_FES GRIDcompulsory keyword 
the action that creates the input grid you would like to use =hh TEMPthe temperature at which you are operating =300 The CONVERT_TO_FES action with label fes
DUMPGRID GRIDcompulsory keyword 
the action that creates the grid you would like to output =fes FILEcompulsory keyword ( default=density )
the file on which to write the grid. =fes.dat The DUMPGRID action with label 

The script above must be run with multiple replicas using the following command:

mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4

Glossary of keywords and components

Compulsory keywords

ARG	the arguments that you would like to make the histogram for
BIAS	( default=*.bias ) the value of the biases to use when performing WHAM
TEMP	the temperature at which the simulation was run
STRIDE	( default=1 ) the frequency with which the data should be stored to perform WHAM
GRID_MIN	the minimum to use for the grid
GRID_MAX	the maximum to use for the grid
GRID_BIN	the number of bins to use for the grid

Options

BANDWIDTH

the bandwidth for kernel density estimation