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Entropy 2017, 19(7), 367; doi:10.3390/e19070367

Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics

1
Institute of Mathematics, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
2
Zuse Institute Berlin, Takustrasse 7, 14195 Berlin, Germany
*
Author to whom correspondence should be addressed.
Received: 25 April 2017 / Revised: 13 July 2017 / Accepted: 13 July 2017 / Published: 18 July 2017
(This article belongs to the Special Issue Understanding Molecular Dynamics via Stochastic Processes)
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Abstract

Many interesting rare events in molecular systems, like ligand association, protein folding or conformational changes, occur on timescales that often are not accessible by direct numerical simulation. Therefore, rare event approximation approaches like interface sampling, Markov state model building, or advanced reaction coordinate-based free energy estimation have attracted huge attention recently. In this article we analyze the reliability of such approaches. How precise is an estimate of long relaxation timescales of molecular systems resulting from various forms of rare event approximation methods? Our results give a theoretical answer to this question by relating it with the transfer operator approach to molecular dynamics. By doing so we also allow for understanding deep connections between the different approaches. View Full-Text
Keywords: molecular dynamics; eigenproblem; effective dynamics; Galerkin method; variational approach; Markov state model; reaction coordinate molecular dynamics; eigenproblem; effective dynamics; Galerkin method; variational approach; Markov state model; reaction coordinate
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Zhang, W.; Schütte, C. Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics. Entropy 2017, 19, 367.

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