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Exchanging Replicas with Unequal Cost, Infinitely and Permanently
[Image: see text] We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different types of processor units or because of the algo...
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/PMC9720720/ https://www.ncbi.nlm.nih.gov/pubmed/36394633 http://dx.doi.org/10.1021/acs.jpca.2c06004 |
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author | Roet, Sander Zhang, Daniel T. van Erp, Titus S. |
author_facet | Roet, Sander Zhang, Daniel T. van Erp, Titus S. |
author_sort | Roet, Sander |
collection | PubMed |
description | [Image: see text] We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different types of processor units or because of the algorithmic complexity. To prove detailed-balance, we make a paradigm shift from the common conceptual viewpoint in which the set of parallel replicas represents a high-dimensional superstate, to an ensemble-based criterion in which the other ensembles represent an environment that might or might not participate in the Monte Carlo move. In addition, based on a recent algorithm for computing permanents, we effectively increase the exchange rate to infinite without the steep factorial scaling as a function of the number of replicas. We illustrate the effectiveness of this replica exchange methodology by combining it with a quantitative path sampling method, replica exchange transition interface sampling (RETIS), in which the costs for a Monte Carlo move can vary enormously as paths in a RETIS algorithm do not have the same length and the average path lengths tend to vary considerably for the different path ensembles that run in parallel. This combination, coined ∞RETIS, was tested on three model systems. |
format | Online Article Text |
id | pubmed-9720720 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-97207202022-12-06 Exchanging Replicas with Unequal Cost, Infinitely and Permanently Roet, Sander Zhang, Daniel T. van Erp, Titus S. J Phys Chem A [Image: see text] We developed a replica exchange method that is effectively parallelizable even if the computational cost of the Monte Carlo moves in the parallel replicas are considerably different, for instance, because the replicas run on different types of processor units or because of the algorithmic complexity. To prove detailed-balance, we make a paradigm shift from the common conceptual viewpoint in which the set of parallel replicas represents a high-dimensional superstate, to an ensemble-based criterion in which the other ensembles represent an environment that might or might not participate in the Monte Carlo move. In addition, based on a recent algorithm for computing permanents, we effectively increase the exchange rate to infinite without the steep factorial scaling as a function of the number of replicas. We illustrate the effectiveness of this replica exchange methodology by combining it with a quantitative path sampling method, replica exchange transition interface sampling (RETIS), in which the costs for a Monte Carlo move can vary enormously as paths in a RETIS algorithm do not have the same length and the average path lengths tend to vary considerably for the different path ensembles that run in parallel. This combination, coined ∞RETIS, was tested on three model systems. American Chemical Society 2022-11-17 2022-12-01 /pmc/articles/PMC9720720/ /pubmed/36394633 http://dx.doi.org/10.1021/acs.jpca.2c06004 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 | Roet, Sander Zhang, Daniel T. van Erp, Titus S. Exchanging Replicas with Unequal Cost, Infinitely and Permanently |
title | Exchanging Replicas with Unequal Cost, Infinitely
and Permanently |
title_full | Exchanging Replicas with Unequal Cost, Infinitely
and Permanently |
title_fullStr | Exchanging Replicas with Unequal Cost, Infinitely
and Permanently |
title_full_unstemmed | Exchanging Replicas with Unequal Cost, Infinitely
and Permanently |
title_short | Exchanging Replicas with Unequal Cost, Infinitely
and Permanently |
title_sort | exchanging replicas with unequal cost, infinitely
and permanently |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9720720/ https://www.ncbi.nlm.nih.gov/pubmed/36394633 http://dx.doi.org/10.1021/acs.jpca.2c06004 |
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