Shortcut: WHAM_WEIGHTS

Module	wham
Description	Usage
Calculate and output weights for configurations using the weighted histogram analysis method.
output value	type
the weights that were calculated using WHAM	vector

Further details and examples

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. The following input demonstrates how this works in practise by showing you how this action 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

#SETTINGS NREPLICAS=4
phi: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=5,7,9,15
The TORSION action with label phi calculates the following quantities:
 Quantity   
 Description  
phi.value
the TORSION involving these atomsrp: RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=phi KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=50.0 ATthe position of the restraint=@replicas:This keyword specifies that different replicas have different values for this quantity.  See here for more details.{-3.00,-1.45,0.10,1.65}
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 potentialWHAM_WEIGHTSCalculate and output weights for configurations using the weighted histogram analysis method. More details BIAS the value of the biases to use when performing WHAM=rp.bias TEMPthe temperature at which the simulation was run=300 FILEthe file on which to output the WHAM weights=wham-weights

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

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

For more details on how the weights for configurations are determined using the wham method see the documentation for the WHAM action.

Syntax

The following table describes the keywords and options that can be used with this action