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

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.

PyEmma tutorial header image
Published
2019-11-29
How to Cite
Wehmeyer, C., Scherer, M. K., Hempel, T., Husic, B. E., Olsson, S., & Noé, F. (2019). Introduction to Markov state modeling with the PyEMMA software [Article v1.0]. Living Journal of Computational Molecular Science, 1(1), 5965. https://doi.org/10.33011/livecoms.1.1.5965
Section
Articles