whampy

whampy is a python3 script that performs a WHAM calculation on umbrella sampling datasets in order to obtain a potential of mean force.

Getting Started

Prerequisites

Disclaimer: program in development

• python3.x must be installed.
• The following python packages must be installed:
  • numpy
  • scipy
  • matplotlib
• These can be installed with pip

whampy instructions

The whampy" program computes the potential of mean force of an umbrella sampling simulation using a minimization of a log-likelihood function of the probability distribution in 1D.

The execution of the program is as follows:

python3 wham.py [-h] [-s] [-i INPUT] [-o OUTPUT]

where the INPUT file is a plain text file with the format as specified in example/example.in. The trajectory files sourced from the paths found in the input file are assumed to be in the two-column NAMD .traj format as shown in the example/example.traj file.

For more information about the options, the [-h] optional flag brings up the help text.

Test execution

A simple calculation of the potential of mean force of the rotation of the C2-C3 dihedral angle of butane is provided for testing purposes.

To execute the test, the following command suffices:

python3 wham.py -i example/input/example.in -o example/output/test

The results of the PMF will then be stored in example/output/test.pmf, with the reaction coordinate in the first column, the PMF value in the second column, and the standard error of the PMF value in the third.

Plotting these results with the first column at the x-axis and the second column at the y-axis will produce results equivalent to those contained in the provided .png file.

=======

The 'montecarlo' branch includes a modified version of the code that also generates a dataset with Monte Carlo, useful for testing.