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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...

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Autores principales: Darkins, Robert, Duffy, Dorothy M., Ford, Ian J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
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.
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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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