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Stochastic Resetting for Enhanced Sampling
[Image: see text] 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 tr...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9743203/ https://www.ncbi.nlm.nih.gov/pubmed/36446130 http://dx.doi.org/10.1021/acs.jpclett.2c03055 |
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author | Blumer, Ofir Reuveni, Shlomi Hirshberg, Barak |
author_facet | Blumer, Ofir Reuveni, Shlomi Hirshberg, Barak |
author_sort | Blumer, Ofir |
collection | PubMed |
description | [Image: see text] 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. |
format | Online Article Text |
id | pubmed-9743203 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-97432032022-12-13 Stochastic Resetting for Enhanced Sampling Blumer, Ofir Reuveni, Shlomi Hirshberg, Barak J Phys Chem Lett [Image: see text] 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. American Chemical Society 2022-11-29 2022-12-08 /pmc/articles/PMC9743203/ /pubmed/36446130 http://dx.doi.org/10.1021/acs.jpclett.2c03055 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Blumer, Ofir Reuveni, Shlomi Hirshberg, Barak Stochastic Resetting for Enhanced Sampling |
title | Stochastic Resetting
for Enhanced Sampling |
title_full | Stochastic Resetting
for Enhanced Sampling |
title_fullStr | Stochastic Resetting
for Enhanced Sampling |
title_full_unstemmed | Stochastic Resetting
for Enhanced Sampling |
title_short | Stochastic Resetting
for Enhanced Sampling |
title_sort | stochastic resetting
for enhanced sampling |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9743203/ https://www.ncbi.nlm.nih.gov/pubmed/36446130 http://dx.doi.org/10.1021/acs.jpclett.2c03055 |
work_keys_str_mv | AT blumerofir stochasticresettingforenhancedsampling AT reuvenishlomi stochasticresettingforenhancedsampling AT hirshbergbarak stochasticresettingforenhancedsampling |