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MasterMSM.pdf (2.23 MB)

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

preprint
submitted on 06.06.2019, 08:40 and posted on 07.06.2019, 15:01 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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