gharib85/mastermsm

Python package for generating Markov state models

MasterMSM

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:

• Create Markov state / master equation models from biomolecular simulations.

• Discretize trajectory data using dihedral angle based methods useful for small peptides.

• Calculate rate matrices using a variety of methods.

• Obtain committors and reactive fluxes.

• Carry out sensitivity analysis of networks.

You can read the documentation here.

Contributors

This code has been written by David De Sancho with help from Anne Aguirre.

Installation

git clone http://github.com/daviddesancho/MasterMSM destination/MasterMSM
cd destination/mastermsm
python setup.py install --user

External libraries

mdtraj : https://mdtraj.org

Citation

@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",
url = "https://chemrxiv.org/articles/MasterMSM_A_Package_for_Constructing_Master_Equation_Models_of_Molecular_Dynamics/8234147",
doi = "10.26434/chemrxiv.8234147.v1"
}