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Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach
Molecular mechanics (MM) is a powerful tool to study the properties of molecular systems in the fields of biology and materials science. With the development of ab initio force field and the application of ab initio potential energy surface, the nuclear quantum effect (NQE) is becoming increasingly...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9161153/ https://www.ncbi.nlm.nih.gov/pubmed/35664679 http://dx.doi.org/10.3389/fmolb.2022.851311 |
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author | Wu, Chuixiong Li, Ruye Yu, Kuang |
author_facet | Wu, Chuixiong Li, Ruye Yu, Kuang |
author_sort | Wu, Chuixiong |
collection | PubMed |
description | Molecular mechanics (MM) is a powerful tool to study the properties of molecular systems in the fields of biology and materials science. With the development of ab initio force field and the application of ab initio potential energy surface, the nuclear quantum effect (NQE) is becoming increasingly important for the robustness of the simulation. However, the state-of-the-art path-integral molecular dynamics simulation, which incorporates NQE in MM, is still too expensive to conduct for most biological and material systems. In this work, we analyze the locality of NQE, using both analytical and numerical approaches, and conclude that NQE is an extremely localized phenomenon in nonreactive molecular systems. Therefore, we can use localized machine learning (ML) models to predict quantum force corrections both accurately and efficiently. Using liquid water as example, we show that the ML facilitated centroid MD can reproduce the NQEs in both the thermodynamical and the dynamical properties, with a minimal increase in computational time compared to classical molecular dynamics. This simple approach thus largely decreases the computational cost of quantum simulations, making it really accessible to the studies of large-scale molecular systems. |
format | Online Article Text |
id | pubmed-9161153 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-91611532022-06-03 Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach Wu, Chuixiong Li, Ruye Yu, Kuang Front Mol Biosci Molecular Biosciences Molecular mechanics (MM) is a powerful tool to study the properties of molecular systems in the fields of biology and materials science. With the development of ab initio force field and the application of ab initio potential energy surface, the nuclear quantum effect (NQE) is becoming increasingly important for the robustness of the simulation. However, the state-of-the-art path-integral molecular dynamics simulation, which incorporates NQE in MM, is still too expensive to conduct for most biological and material systems. In this work, we analyze the locality of NQE, using both analytical and numerical approaches, and conclude that NQE is an extremely localized phenomenon in nonreactive molecular systems. Therefore, we can use localized machine learning (ML) models to predict quantum force corrections both accurately and efficiently. Using liquid water as example, we show that the ML facilitated centroid MD can reproduce the NQEs in both the thermodynamical and the dynamical properties, with a minimal increase in computational time compared to classical molecular dynamics. This simple approach thus largely decreases the computational cost of quantum simulations, making it really accessible to the studies of large-scale molecular systems. Frontiers Media S.A. 2022-05-19 /pmc/articles/PMC9161153/ /pubmed/35664679 http://dx.doi.org/10.3389/fmolb.2022.851311 Text en Copyright © 2022 Wu, Li and Yu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Molecular Biosciences Wu, Chuixiong Li, Ruye Yu, Kuang Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach |
title | Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach |
title_full | Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach |
title_fullStr | Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach |
title_full_unstemmed | Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach |
title_short | Learning the Quantum Centroid Force Correction in Molecular Systems: A Localized Approach |
title_sort | learning the quantum centroid force correction in molecular systems: a localized approach |
topic | Molecular Biosciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9161153/ https://www.ncbi.nlm.nih.gov/pubmed/35664679 http://dx.doi.org/10.3389/fmolb.2022.851311 |
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