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Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters
[Image: see text] Molecular simulations based on classical force fields are computationally efficient but lack accuracy due to the empirical formulation of non-bonded interactions. Quantum mechanical (QM) methods, albeit accurate, have inhibitory computational costs for large molecules and clusters....
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143414/ https://www.ncbi.nlm.nih.gov/pubmed/32280847 http://dx.doi.org/10.1021/acsomega.9b02968 |
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author | Bose, Samik Chakrabarty, Suman Ghosh, Debashree |
author_facet | Bose, Samik Chakrabarty, Suman Ghosh, Debashree |
author_sort | Bose, Samik |
collection | PubMed |
description | [Image: see text] Molecular simulations based on classical force fields are computationally efficient but lack accuracy due to the empirical formulation of non-bonded interactions. Quantum mechanical (QM) methods, albeit accurate, have inhibitory computational costs for large molecules and clusters. Hence, to overcome the bottleneck, machine learning (ML)-based methods have been employed in the recent years. We had earlier reported a combined scheme of many-body expansion (MBE) and ML to predict the interaction energies of rigid water clusters. In this work, we proceed toward building a flexible water model using the ML-MBE scheme. This ML-MBE scheme has an error of <1% for interaction energy prediction in comparison to the parent QM method for flexible water decamers. Machine learning-based Monte Carlo simulations (MLMC) are performed with this water model, and the structural properties of these configurations are compared with those obtained from ab initio molecular dynamics (AIMD) and the TIP3P classical force field. The radial distribution functions, tetrahedral order parameters, and number of hydrogen bonds in AIMD and MLMC have a similar qualitative and quantitative trend, whereas the classical force fields show a significant deviation. |
format | Online Article Text |
id | pubmed-7143414 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-71434142020-04-10 Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters Bose, Samik Chakrabarty, Suman Ghosh, Debashree ACS Omega [Image: see text] Molecular simulations based on classical force fields are computationally efficient but lack accuracy due to the empirical formulation of non-bonded interactions. Quantum mechanical (QM) methods, albeit accurate, have inhibitory computational costs for large molecules and clusters. Hence, to overcome the bottleneck, machine learning (ML)-based methods have been employed in the recent years. We had earlier reported a combined scheme of many-body expansion (MBE) and ML to predict the interaction energies of rigid water clusters. In this work, we proceed toward building a flexible water model using the ML-MBE scheme. This ML-MBE scheme has an error of <1% for interaction energy prediction in comparison to the parent QM method for flexible water decamers. Machine learning-based Monte Carlo simulations (MLMC) are performed with this water model, and the structural properties of these configurations are compared with those obtained from ab initio molecular dynamics (AIMD) and the TIP3P classical force field. The radial distribution functions, tetrahedral order parameters, and number of hydrogen bonds in AIMD and MLMC have a similar qualitative and quantitative trend, whereas the classical force fields show a significant deviation. American Chemical Society 2020-03-24 /pmc/articles/PMC7143414/ /pubmed/32280847 http://dx.doi.org/10.1021/acsomega.9b02968 Text en Copyright © 2020 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Bose, Samik Chakrabarty, Suman Ghosh, Debashree Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters |
title | Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters |
title_full | Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters |
title_fullStr | Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters |
title_full_unstemmed | Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters |
title_short | Support Vector Regression-Based Monte Carlo Simulation of Flexible Water Clusters |
title_sort | support vector regression-based monte carlo simulation of flexible water clusters |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7143414/ https://www.ncbi.nlm.nih.gov/pubmed/32280847 http://dx.doi.org/10.1021/acsomega.9b02968 |
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