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Coarse-Grained Modeling Using Neural Networks Trained on Structural Data
[Image: see text] We propose a method of bottom-up coarse-graining, in which interactions within a coarse-grained model are determined by an artificial neural network trained on structural data obtained from multiple atomistic simulations. The method uses ideas of the inverse Monte Carlo approach, r...
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/PMC10569054/ https://www.ncbi.nlm.nih.gov/pubmed/37712507 http://dx.doi.org/10.1021/acs.jctc.3c00516 |
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author | Ivanov, Mikhail Posysoev, Maksim Lyubartsev, Alexander P. |
author_facet | Ivanov, Mikhail Posysoev, Maksim Lyubartsev, Alexander P. |
author_sort | Ivanov, Mikhail |
collection | PubMed |
description | [Image: see text] We propose a method of bottom-up coarse-graining, in which interactions within a coarse-grained model are determined by an artificial neural network trained on structural data obtained from multiple atomistic simulations. The method uses ideas of the inverse Monte Carlo approach, relating changes in the neural network weights with changes in average structural properties, such as radial distribution functions. As a proof of concept, we demonstrate the method on a system interacting by a Lennard–Jones potential modeled by a simple linear network and a single-site coarse-grained model of methanol–water solutions. In the latter case, we implement a nonlinear neural network with intermediate layers trained by atomistic simulations carried out at different methanol concentrations. We show that such a network acts as a transferable potential at the coarse-grained resolution for a wide range of methanol concentrations, including those not included in the training set. |
format | Online Article Text |
id | pubmed-10569054 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-105690542023-10-13 Coarse-Grained Modeling Using Neural Networks Trained on Structural Data Ivanov, Mikhail Posysoev, Maksim Lyubartsev, Alexander P. J Chem Theory Comput [Image: see text] We propose a method of bottom-up coarse-graining, in which interactions within a coarse-grained model are determined by an artificial neural network trained on structural data obtained from multiple atomistic simulations. The method uses ideas of the inverse Monte Carlo approach, relating changes in the neural network weights with changes in average structural properties, such as radial distribution functions. As a proof of concept, we demonstrate the method on a system interacting by a Lennard–Jones potential modeled by a simple linear network and a single-site coarse-grained model of methanol–water solutions. In the latter case, we implement a nonlinear neural network with intermediate layers trained by atomistic simulations carried out at different methanol concentrations. We show that such a network acts as a transferable potential at the coarse-grained resolution for a wide range of methanol concentrations, including those not included in the training set. American Chemical Society 2023-09-15 /pmc/articles/PMC10569054/ /pubmed/37712507 http://dx.doi.org/10.1021/acs.jctc.3c00516 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 | Ivanov, Mikhail Posysoev, Maksim Lyubartsev, Alexander P. Coarse-Grained Modeling Using Neural Networks Trained on Structural Data |
title | Coarse-Grained
Modeling Using Neural Networks Trained
on Structural Data |
title_full | Coarse-Grained
Modeling Using Neural Networks Trained
on Structural Data |
title_fullStr | Coarse-Grained
Modeling Using Neural Networks Trained
on Structural Data |
title_full_unstemmed | Coarse-Grained
Modeling Using Neural Networks Trained
on Structural Data |
title_short | Coarse-Grained
Modeling Using Neural Networks Trained
on Structural Data |
title_sort | coarse-grained
modeling using neural networks trained
on structural data |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569054/ https://www.ncbi.nlm.nih.gov/pubmed/37712507 http://dx.doi.org/10.1021/acs.jctc.3c00516 |
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