grand : Grand Canonical Sampling of Waters in OpenMM

Background

This Python module is designed to be run with OpenMM in order to simulate grand canonical Monte Carlo (GCMC) insertion and deletion moves of water molecules. This allows the particle number to vary according to a fixed chemical potential, and offers enhanced sampling of water molecules in occluded binding sites. The theory behind our work on GCMC sampling can be found in the References section below.

Installation & Usage

This module can be installed from this directory by running the following command:

python setup.py install

The dependencies of this module can be installed as:

conda install -c omnia openmm mdtraj parmed openmmtools pymbar
pip install lxml

The grand module is released under the MIT licence. If results from this module contribute to a publication, we only ask that you cite the publications below.

Contributors

  • Marley Samways <mls2g13@soton.ac.uk>

  • Hannah Bruce Macdonald <hannah.brucemacdonald@choderalab.org>

Contact

If you have any problems or questions regarding this module, please contact one of the contributors, or send an email to <jessexgroup@gmail.com>.

References

1. G. A. Ross, M. S. Bodnarchuk, J. W. Essex, J. Am. Chem. Soc. 2015, 137, 47, 14930-14943, DOI: https://doi.org/10.1021/jacs.5b07940

2. G. A. Ross, H. E. Bruce Macdonald, C. Cave-Ayland, A. I. Cabedo Martinez, J. W. Essex, J. Chem. Theory Comput. 2017, 13, 12, 6373-6381, DOI: https://doi.org/10.1021/acs.jctc.7b00738