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Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids
[Image: see text] Current machine learning (ML) models aimed at learning force fields are plagued by their high computational cost at every integration time step. We describe a number of practical and computationally efficient strategies to parametrize traditional force fields for molecular liquids...
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/PMC7304872/ https://www.ncbi.nlm.nih.gov/pubmed/32282206 http://dx.doi.org/10.1021/acs.jctc.9b01256 |
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author | Scherer, Christoph Scheid, René Andrienko, Denis Bereau, Tristan |
author_facet | Scherer, Christoph Scheid, René Andrienko, Denis Bereau, Tristan |
author_sort | Scherer, Christoph |
collection | PubMed |
description | [Image: see text] Current machine learning (ML) models aimed at learning force fields are plagued by their high computational cost at every integration time step. We describe a number of practical and computationally efficient strategies to parametrize traditional force fields for molecular liquids from ML: the particle decomposition ansatz to two- and three-body force fields, the use of kernel-based ML models that incorporate physical symmetries, the incorporation of switching functions close to the cutoff, and the use of covariant meshing to boost the training set size. Results are presented for model molecular liquids: pairwise Lennard-Jones, three-body Stillinger–Weber, and bottom-up coarse-graining of water. Here, covariant meshing proves to be an efficient strategy to learn canonically averaged instantaneous forces. We show that molecular dynamics simulations with tabulated two- and three-body ML potentials are computationally efficient and recover two- and three-body distribution functions. Many-body representations, decomposition, and kernel regression schemes are all implemented in the open-source software package VOTCA. |
format | Online Article Text |
id | pubmed-7304872 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-73048722020-06-22 Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids Scherer, Christoph Scheid, René Andrienko, Denis Bereau, Tristan J Chem Theory Comput [Image: see text] Current machine learning (ML) models aimed at learning force fields are plagued by their high computational cost at every integration time step. We describe a number of practical and computationally efficient strategies to parametrize traditional force fields for molecular liquids from ML: the particle decomposition ansatz to two- and three-body force fields, the use of kernel-based ML models that incorporate physical symmetries, the incorporation of switching functions close to the cutoff, and the use of covariant meshing to boost the training set size. Results are presented for model molecular liquids: pairwise Lennard-Jones, three-body Stillinger–Weber, and bottom-up coarse-graining of water. Here, covariant meshing proves to be an efficient strategy to learn canonically averaged instantaneous forces. We show that molecular dynamics simulations with tabulated two- and three-body ML potentials are computationally efficient and recover two- and three-body distribution functions. Many-body representations, decomposition, and kernel regression schemes are all implemented in the open-source software package VOTCA. American Chemical Society 2020-04-13 2020-05-12 /pmc/articles/PMC7304872/ /pubmed/32282206 http://dx.doi.org/10.1021/acs.jctc.9b01256 Text en Copyright © 2020 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
spellingShingle | Scherer, Christoph Scheid, René Andrienko, Denis Bereau, Tristan Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids |
title | Kernel-Based Machine Learning for Efficient Simulations
of Molecular Liquids |
title_full | Kernel-Based Machine Learning for Efficient Simulations
of Molecular Liquids |
title_fullStr | Kernel-Based Machine Learning for Efficient Simulations
of Molecular Liquids |
title_full_unstemmed | Kernel-Based Machine Learning for Efficient Simulations
of Molecular Liquids |
title_short | Kernel-Based Machine Learning for Efficient Simulations
of Molecular Liquids |
title_sort | kernel-based machine learning for efficient simulations
of molecular liquids |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304872/ https://www.ncbi.nlm.nih.gov/pubmed/32282206 http://dx.doi.org/10.1021/acs.jctc.9b01256 |
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