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MasterMSM.pdf (2.23 MB)

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

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


Email Address of Submitting Author


University of the Basque Country / Donostia International Physics Center



ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict of interest


Read the published paper

in Journal of Chemical Information and Modeling