MasterMSM is a Python package for generating Markov state models (MSMs) from molecular dynamics trajectories. We use a formulation based on the chemical master equation. This package will allow you to:
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Create Markov state / master equation models from biomolecular simulations.
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Discretize trajectory data using dihedral angle based methods useful for small peptides.
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Calculate rate matrices using a variety of methods.
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Obtain committors and reactive fluxes.
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Carry out sensitivity analysis of networks.
You can read the documentation here.
This code has been written by David De Sancho with help from Anne Aguirre.
Requires Python >= 3.10. Install from source:
git clone https://github.com/BioKT/MasterMSM
cd MasterMSM
pip install .
For development (editable install):
pip install -e .
- numpy
- scipy
- matplotlib
- networkx
- mdtraj (https://mdtraj.org)
- scikit-learn
@article{mastermsm,
author = "David De Sancho and Anne Aguirre",
title = "{MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics}",
year = "2019",
month = "6",
journal = "J. Chem. Inf. Model.",
url = "https://doi.org/10.1021/acs.jcim.9b00468",
doi = "10.1021/acs.jcim.9b00468"
}