grand : Grand Canonical Sampling of Waters in OpenMM¶
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.
Marley Samways <firstname.lastname@example.org>
Hannah Bruce Macdonald <email@example.com>
If you have any problems or questions regarding this module, please contact one of the contributors, or send an email to <firstname.lastname@example.org>.
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