Introduction to Markov state modeling with the PyEMMA software [Article v1.0]

Christoph Wehmeyer; Martin K. Scherer; Tim Hempel; Brooke E. Husic; Simon Olsson; Frank Noé

doi:10.33011/livecoms.1.1.5965

Authors

Christoph Wehmeyer Department of Mathematics and Computer Science, Freie Universität Berlin https://orcid.org/0000-0002-9526-0328
Martin K. Scherer Department of Mathematics and Computer Science, Freie Universität Berlin https://orcid.org/0000-0002-7983-4387
Tim Hempel Department of Mathematics and Computer Science, Freie Universität Berlin https://orcid.org/0000-0002-0073-9353
Brooke E. Husic Stanford University, Department of Chemistry and Freie Universität Berlin, Department of Mathematics and Computer Science https://orcid.org/0000-0002-8020-3750
Simon Olsson Department of Mathematics and Computer Science, Freie Universität Berlin https://orcid.org/0000-0002-3927-7897
Frank Noé Department of Mathematics and Computer Science, Freie Universität Berlin and Department of Chemistry,Rice University https://orcid.org/0000-0003-4169-9324

DOI:

https://doi.org/10.33011/livecoms.1.1.5965

Keywords:

molecular dynamics, markov state model, msm, pyemma

Abstract

This tutorial provides an introduction to the construction of Markov models of molecular kinetics from molecular dynamics trajectory data with the PyEMMA software. Using tutorial notebooks, we will guide the user through the basic functionality as well as the more common advanced mechanisms. Short exercises to self check the learning progress and a notebook on troubleshooting complete this basic introduction.

Introduction to Markov state modeling with the PyEMMA software [Article v1.0]

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