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 
ATOMS
the four atoms involved in the torsional angle 
=5,7,9,15 The TORSION action with label phi calculates a single scalar value
psi: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=7,9,15,17 The TORSION action with label psi calculates a single scalar value
rp: RESTRAINT 
ARG
the arguments on which the bias is acting. 
=phi 
KAPPA
compulsory 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 
   
AT
compulsory 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 
ARG
compulsory keyword 
the arguments that you would like to make the histogram for 
=phi 
BIAS
compulsory keyword ( default=*.bias )
the value of the biases to use when performing WHAM 
=rp.bias 
TEMP
compulsory keyword 
the temperature at which the simulation was run 
=300 
GRID_MIN
compulsory keyword 
the minimum to use for the grid 
=-pi 
GRID_MAX
compulsory keyword 
the maximum to use for the grid 
=pi 
GRID_BIN
compulsory keyword 
the number of bins to use for the grid 
=50 The WHAM_HISTOGRAM action with label hh calculates a single scalar value
fes: CONVERT_TO_FES 
GRID
the histogram that you would like to convert into a free energy surface (old syntax)
=hh 
TEMP
the temperature at which you are operating 
=300 The CONVERT_TO_FES action with label fes calculates a single scalar value
DUMPGRID 
GRID
the grid you would like to print (can also use ARG for specifying what is being printed)
=fes 
FILE
compulsory keyword ( default=density )
the file on which to write the grid. 
=fes.dat The DUMPGRID action with label 

#SETTINGS NREPLICAS=4
phi: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=5,7,9,15 The TORSION action with label phi calculates a single scalar value
psi: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=7,9,15,17 The TORSION action with label psi calculates a single scalar value
rp: RESTRAINT_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=phi 
KAPPA
compulsory 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 
AT
compulsory keyword 
the position of the restraint 
=@replicas:,-3.00000000000000000000,-1.45161290322580645168,.09677419354838709664,1.64516129032258064496 The RESTRAINT_SCALAR action with label rp
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