This Python module is designed to be run with OpenMM in order to simulate grand canonical Monte Carlo (GCMC) and nonequilibirum candidate Monte Carlo (GCNCMC) insertion and deletion moves of ligand and water molecules. This allows the particle number to vary according to a fixed chemical potential, and offers enhanced sampling of molecules in occluded binding sites.
The theory behind our work on GCMC sampling can be found in the References section below.
A suitable conda environment is provided in grand_env.yaml. We recommend making a new environment from the .yaml file.
This module can be installed from this directory by running the following command (conda coming soon):
pip install .
The tests can be carried out by running the following command from this directory:
pytest -v grandlig/tests/
Please note, these tests may take a while as they are configured to run on the CPU platform (Up to 2hrs).
Several (short) examples of how this module is ran alongside OpenMM can be found in
the examples/ directory.
Additional examples and
documentation are also available.
The grandlig module is released under the MIT licence.
If results from this module contribute to a publication, we ask that you cite the following publications:
- PLACEHOLDER FOR PAPER
- O. J. Melling, M. L. Samways, Y. Ge, D. L. Mobley, J. W. Essex, J. Chem. Theory Comput., 2023, DOI: https://doi.org/10.1021/acs.jctc.2c00823
- M. L. Samways, H. E. Bruce Macdonald, J. W. Essex, J. Chem. Inf. Model., 2020, 60, 4436-4441, DOI: https://doi.org/10.1021/acs.jcim.0c00648
Ref. 1 discusses the initial implemention of ligand-based GCNCMC. Ref. 2 discusses the implementation and testing of the non-equilibrium moves with water molecules. Ref. 3 describes the original implementation of grand from which this work stems from.
Additional references describing the theory upon which the GCNCMC implemention in grandlig is based are also provided below.
- Will Poole
<wp1g16@soton.ac.uk> - Marley Samways
<mls2g13@soton.ac.uk> - Ollie Melling
<ojm2g16@soton.ac.uk>
If you have any problems or questions regarding this module, please raise a github issue or contact
one of the contributors, or send an email to <j.w.essex@soton.ac.uk>.
- M. L. Samways, H. E. Bruce Macdonald, J. W. Essex, J. Chem. Inf. Model., 2020, 60, 4436-4441, DOI: https://doi.org/10.1021/acs.jcim.0c00648
- O. J. Melling, M. L. Samways, Y. Ge, D. L. Mobley, J. W. Essex, J. Chem. Theory Comput., 2023, DOI: https://doi.org/10.1021/acs.jctc.2c00823
- 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
- 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
Copyright (c) 2024, Will Poole
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