Set-free Markov State Building

Please always quote using this URN: urn:nbn:de:0297-zib-62167
  • Molecular dynamics (MD) simulations face challenging problems since the timescales of interest often are much longer than what is possible to simulate and even if sufficiently long simulation are possible the complex nature of the resulting simulation data makes interpretation difficult. Markov State Models (MSMs) help to overcome these problems by making experimentally relevant timescales accessible via coarse grained representations that also allows for convenient interpretation. However, standard set-based MSMs exhibit some caveats limiting their approximation quality and statistical significance. One of the main caveats results from the fact that typical MD trajectories repeatedly re-cross the boundary between the sets used to build the MSM which causes statistical bias in estimating the transition probabilities between these sets. In this article, we present a set-free approach to MSM building utilizing smooth overlapping ansatz functions instead of sets and an adaptive refinement approach. This kind of meshless discretization helps to overcome the recrossing problem and yields an adaptive refinement procedure that allows to improve the quality of the model while exploring state space and inserting new ansatz functions into the MSM.

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Author:Marcus Weber, Konstantin Fackeldey, Christof Schütte
Document Type:ZIB-Report
Date of first Publication:2017/03/03
Series (Serial Number):ZIB-Report (17-10)
Published in:Appeared in: Journal of Chemical Physics 146/12 (2017)

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