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Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions
[Image: see text] Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems....
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/PMC9878731/ https://www.ncbi.nlm.nih.gov/pubmed/36633918 http://dx.doi.org/10.1021/acs.jctc.2c00661 |
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author | Thürlemann, Moritz Böselt, Lennard Riniker, Sereina |
author_facet | Thürlemann, Moritz Böselt, Lennard Riniker, Sereina |
author_sort | Thürlemann, Moritz |
collection | PubMed |
description | [Image: see text] Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems. The parametrization of FF is, however, time-consuming and has traditionally been based on experimental data. Recent years have therefore seen increasing efforts to automatize FF parametrization or to replace FF with machine-learning (ML) based potentials. Here, we propose an alternative strategy to parametrize FF, which makes use of ML and gradient-descent based optimization while retaining a functional form founded in physics. Using a predefined functional form is shown to enable interpretability, robustness, and efficient simulations of large systems over long time scales. To demonstrate the strength of the proposed method, a fixed-charge and a polarizable model are trained on ab initio potential-energy surfaces. Given only information about the constituting elements, the molecular topology, and reference potential energies, the models successfully learn to assign atom types and corresponding FF parameters from scratch. The resulting models and parameters are validated on a wide range of experimentally and computationally derived properties of systems including dimers, pure liquids, and molecular crystals. |
format | Online Article Text |
id | pubmed-9878731 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-98787312023-01-27 Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions Thürlemann, Moritz Böselt, Lennard Riniker, Sereina J Chem Theory Comput [Image: see text] Simulations of molecular systems using electronic structure methods are still not feasible for many systems of biological importance. As a result, empirical methods such as force fields (FF) have become an established tool for the simulation of large and complex molecular systems. The parametrization of FF is, however, time-consuming and has traditionally been based on experimental data. Recent years have therefore seen increasing efforts to automatize FF parametrization or to replace FF with machine-learning (ML) based potentials. Here, we propose an alternative strategy to parametrize FF, which makes use of ML and gradient-descent based optimization while retaining a functional form founded in physics. Using a predefined functional form is shown to enable interpretability, robustness, and efficient simulations of large systems over long time scales. To demonstrate the strength of the proposed method, a fixed-charge and a polarizable model are trained on ab initio potential-energy surfaces. Given only information about the constituting elements, the molecular topology, and reference potential energies, the models successfully learn to assign atom types and corresponding FF parameters from scratch. The resulting models and parameters are validated on a wide range of experimentally and computationally derived properties of systems including dimers, pure liquids, and molecular crystals. American Chemical Society 2023-01-12 /pmc/articles/PMC9878731/ /pubmed/36633918 http://dx.doi.org/10.1021/acs.jctc.2c00661 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Thürlemann, Moritz Böselt, Lennard Riniker, Sereina Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions |
title | Regularized by Physics: Graph Neural Network Parametrized
Potentials for the Description of Intermolecular Interactions |
title_full | Regularized by Physics: Graph Neural Network Parametrized
Potentials for the Description of Intermolecular Interactions |
title_fullStr | Regularized by Physics: Graph Neural Network Parametrized
Potentials for the Description of Intermolecular Interactions |
title_full_unstemmed | Regularized by Physics: Graph Neural Network Parametrized
Potentials for the Description of Intermolecular Interactions |
title_short | Regularized by Physics: Graph Neural Network Parametrized
Potentials for the Description of Intermolecular Interactions |
title_sort | regularized by physics: graph neural network parametrized
potentials for the description of intermolecular interactions |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9878731/ https://www.ncbi.nlm.nih.gov/pubmed/36633918 http://dx.doi.org/10.1021/acs.jctc.2c00661 |
work_keys_str_mv | AT thurlemannmoritz regularizedbyphysicsgraphneuralnetworkparametrizedpotentialsforthedescriptionofintermolecularinteractions AT boseltlennard regularizedbyphysicsgraphneuralnetworkparametrizedpotentialsforthedescriptionofintermolecularinteractions AT rinikersereina regularizedbyphysicsgraphneuralnetworkparametrizedpotentialsforthedescriptionofintermolecularinteractions |