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

#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

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