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Stochastic Resetting for Enhanced Sampling.

ABSTRACT: We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on time scales that are unreachable in standard simulations. They are often characterized by broad transition time distributions, in which extremely slow events have a non-negligible probability. Stochastic resetting, i.e., restarting simulations at random times, was recently shown to significantly expedite processes that follow such distributions. Here, we employ resetting for enhanced sampling of molecular simulations for the first time. We show that it accelerates long time scale processes by up to an order of magnitude in examples ranging from simple models to a molecular system. Most importantly, we recover the mean transition time without resetting, which is typically too long to be sampled directly, from accelerated simulations at a single restart rate. Stochastic resetting can be used as a standalone method or combined with other sampling algorithms to further accelerate simulations.

SUBMITTER: Blumer O

PROVIDER: S-EPMC9743203 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Stochastic Resetting for Enhanced Sampling.

Blumer Ofir O Reuveni Shlomi S Hirshberg Barak B

The journal of physical chemistry letters 20221129 48

We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on time scales that are unreachable in standard simulations. They are often characterized by broad transition time distributions, in which extremely slow events have a non-negligible probability. Stochastic resetting, i.e., restarting simulations at random times, was recently shown to significantly expedite processes ...[more]

PMID: 36446130

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Stochastic Resetting for Enhanced Sampling.

Publications

Stochastic Resetting for Enhanced Sampling.

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