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Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling
[Image: see text] Molecular reactions in solution typically involve solvent exchange; for example, a surface must partly desolvate for a molecule to adsorb onto it. When these reactions are simulated, slow solvent dynamics can limit the sampling of configurations and reduce the accuracy of free ener...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10653078/ https://www.ncbi.nlm.nih.gov/pubmed/37864561 http://dx.doi.org/10.1021/acs.jctc.3c00786 |
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author | Darkins, Robert Duffy, Dorothy M. Ford, Ian J. |
author_facet | Darkins, Robert Duffy, Dorothy M. Ford, Ian J. |
author_sort | Darkins, Robert |
collection | PubMed |
description | [Image: see text] Molecular reactions in solution typically involve solvent exchange; for example, a surface must partly desolvate for a molecule to adsorb onto it. When these reactions are simulated, slow solvent dynamics can limit the sampling of configurations and reduce the accuracy of free energy estimates. Here, we combine Hamiltonian replica exchange (HREX) with well-tempered metadynamics (WTMD) to accelerate the sampling of solvent configurations orthogonal to the collective variable space. We compute the formation free energy of a carbonate vacancy in the calcite–water interface and find that the combination of WTMD with HREX significantly improves the sampling relative to WTMD without HREX. |
format | Online Article Text |
id | pubmed-10653078 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-106530782023-11-16 Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling Darkins, Robert Duffy, Dorothy M. Ford, Ian J. J Chem Theory Comput [Image: see text] Molecular reactions in solution typically involve solvent exchange; for example, a surface must partly desolvate for a molecule to adsorb onto it. When these reactions are simulated, slow solvent dynamics can limit the sampling of configurations and reduce the accuracy of free energy estimates. Here, we combine Hamiltonian replica exchange (HREX) with well-tempered metadynamics (WTMD) to accelerate the sampling of solvent configurations orthogonal to the collective variable space. We compute the formation free energy of a carbonate vacancy in the calcite–water interface and find that the combination of WTMD with HREX significantly improves the sampling relative to WTMD without HREX. American Chemical Society 2023-10-21 /pmc/articles/PMC10653078/ /pubmed/37864561 http://dx.doi.org/10.1021/acs.jctc.3c00786 Text en © 2023 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 | Darkins, Robert Duffy, Dorothy M. Ford, Ian J. Accelerating Solvent Dynamics with Replica Exchange for Improved Free Energy Sampling |
title | Accelerating Solvent
Dynamics with Replica Exchange
for Improved Free Energy Sampling |
title_full | Accelerating Solvent
Dynamics with Replica Exchange
for Improved Free Energy Sampling |
title_fullStr | Accelerating Solvent
Dynamics with Replica Exchange
for Improved Free Energy Sampling |
title_full_unstemmed | Accelerating Solvent
Dynamics with Replica Exchange
for Improved Free Energy Sampling |
title_short | Accelerating Solvent
Dynamics with Replica Exchange
for Improved Free Energy Sampling |
title_sort | accelerating solvent
dynamics with replica exchange
for improved free energy sampling |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10653078/ https://www.ncbi.nlm.nih.gov/pubmed/37864561 http://dx.doi.org/10.1021/acs.jctc.3c00786 |
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