WHAM_WEIGHTS

This is part of the analysis module

Calculate and output weights for configurations using the weighted histogram analysis method.

This shortcut action allows you to calculate and output weights computed using the weighted histogram analysis technique. For more detail on how this technique works 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.

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
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


WHAM_WEIGHTS 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 FILEcompulsory keyword 
the file on which to output the WHAM weights =wham-weights The WHAM_WEIGHTS 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
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


@3_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 @3_weights calculates a single scalar value
@3_collect: COLLECT_FRAMES LOGWEIGHTSlist of actions that calculates log weights that should be used to weight configurations
when calculating averages =@3_weights STRIDEthe frequency with which data should be stored for analysis. =1 The COLLECT_FRAMES action with label @3_collect
OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROMuse the output of the analysis performed by this object as input to your new analysis
object =@3_collect FILEcompulsory keyword 
the name of the file to output to =wham-weights FMTthe format to output the data using =%f The OUTPUT_ANALYSIS_DATA_TO_COLVAR 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

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 bias should be stored to perform WHAM
FILE	the file on which to output the WHAM weights

Options

FMT	the format to use for the real numbers in the output file