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arXiv · 1910.07894

Dynamical reweighting methods for Markov models

Stefanie Kieninger·Luca Donati·Bettina G. Keller
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Abstract

Markov State Models (MSM) are widely used to elucidate dynamic properties of molecular systems from unbiased Molecular Dynamics (MD). However, the implementation of reweighting schemes for MSMs to analyze biased simulations, for example produced by enhanced sampling techniques, is still at an early stage of development. Several dynamical reweighing approaches have been proposed, which can be classified as approaches based on (i) Kramers rate theory, (ii) rescaling of the probability density flux, (iii) reweighting by formulating a likelihood function, (iv) path reweighting. We present the state-of-the-art and discuss the methodological differences of these methods, their limitations and recent applications.

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Stefanie Kieninger, Luca Donati, Bettina G. Keller. 2019-10-17. Dynamical reweighting methods for Markov models. https://doi.org/10.1016/j.sbi.2019.12.018

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