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
=5,7,9,15 The TORSION action with label phi calculates a single scalar valuepsi: TORSION
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17 The TORSION action with label psi calculates a single scalar valuerp: RESTRAINT
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 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
=5,7,9,15 The TORSION action with label phi calculates a single scalar valuepsi: TORSION
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17 The TORSION action with label psi calculates a single scalar valuerp: RESTRAINT
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 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