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MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics

preprint
submitted on 06.06.2019 and posted on 07.06.2019 by David De Sancho, Anne Aguirre
Markov state models (MSMs) have become one of the most important techniques for understanding biomolecular transitions from classical molecular dynamics (MD) simulations. MSMs provide a systematized way of accessing the long time kinetics of the system of interest from the short-timescale microscopic transitions observed in simulation trajectories. At the same time, they provide a consistent description of the equilibrium and dynamical properties of the system of interest, and they are ideally suited for comparisons against experiment. A few software packages exist for building MSMs, which have been widely adopted. Here we introduce MasterMSM, a new Python package that uses the master equation formulation of MSMs and provides a number of new algorithms for building and analyzing these models. We demonstrate some of the most distinctive features of the package, including the estimation of rates, definition of core-sets for transition based assignment of states, the estimation of committors and fluxes, and the sensitivity analysis of the emerging networks. The package is available at https://github.com/daviddesancho/MasterMSM.

History

Email Address of Submitting Author

david.desancho@ehu.eus

Institution

University of the Basque Country / Donostia International Physics Center

Country

Spain

ORCID For Submitting Author

0000-0002-8985-2685

Declaration of Conflict of Interest

No conflict of interest

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in Journal of Chemical Information and Modeling

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