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Reducing the Cost of Neural Network Potential Generation for Reactive Molecular Systems
[Image: see text] Although machine learning potentials have recently had a substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio simulation that covers all the relevant geo...
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/PMC10569056/ https://www.ncbi.nlm.nih.gov/pubmed/37747971 http://dx.doi.org/10.1021/acs.jctc.3c00391 |
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author | Brezina, Krystof Beck, Hubert Marsalek, Ondrej |
author_facet | Brezina, Krystof Beck, Hubert Marsalek, Ondrej |
author_sort | Brezina, Krystof |
collection | PubMed |
description | [Image: see text] Although machine learning potentials have recently had a substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio simulation that covers all the relevant geometries of the system. Recognizing that this can be prohibitive for certain systems, we develop the method of transition tube sampling that mitigates the computational cost of training set and model generation. In this approach, we generate classical or quantum thermal geometries around a transition path describing a conformational change or a chemical reaction using only a sparse set of local normal mode expansions along this path and select from these geometries by an active learning protocol. This yields a training set with geometries that characterize the whole transition without the need for a costly reference trajectory. The performance of the method is evaluated on different molecular systems with the complexity of the potential energy landscape increasing from a single minimum to a double proton-transfer reaction with high barriers. Our results show that the method leads to training sets that give rise to models applicable in classical and path integral simulations alike that are on par with those based directly on ab initio calculations while providing the computational speedup we have come to expect from machine learning potentials. |
format | Online Article Text |
id | pubmed-10569056 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-105690562023-10-13 Reducing the Cost of Neural Network Potential Generation for Reactive Molecular Systems Brezina, Krystof Beck, Hubert Marsalek, Ondrej J Chem Theory Comput [Image: see text] Although machine learning potentials have recently had a substantial impact on molecular simulations, the construction of a robust training set can still become a limiting factor, especially due to the requirement of a reference ab initio simulation that covers all the relevant geometries of the system. Recognizing that this can be prohibitive for certain systems, we develop the method of transition tube sampling that mitigates the computational cost of training set and model generation. In this approach, we generate classical or quantum thermal geometries around a transition path describing a conformational change or a chemical reaction using only a sparse set of local normal mode expansions along this path and select from these geometries by an active learning protocol. This yields a training set with geometries that characterize the whole transition without the need for a costly reference trajectory. The performance of the method is evaluated on different molecular systems with the complexity of the potential energy landscape increasing from a single minimum to a double proton-transfer reaction with high barriers. Our results show that the method leads to training sets that give rise to models applicable in classical and path integral simulations alike that are on par with those based directly on ab initio calculations while providing the computational speedup we have come to expect from machine learning potentials. American Chemical Society 2023-09-25 /pmc/articles/PMC10569056/ /pubmed/37747971 http://dx.doi.org/10.1021/acs.jctc.3c00391 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 | Brezina, Krystof Beck, Hubert Marsalek, Ondrej Reducing the Cost of Neural Network Potential Generation for Reactive Molecular Systems |
title | Reducing the Cost of Neural Network Potential Generation
for Reactive Molecular Systems |
title_full | Reducing the Cost of Neural Network Potential Generation
for Reactive Molecular Systems |
title_fullStr | Reducing the Cost of Neural Network Potential Generation
for Reactive Molecular Systems |
title_full_unstemmed | Reducing the Cost of Neural Network Potential Generation
for Reactive Molecular Systems |
title_short | Reducing the Cost of Neural Network Potential Generation
for Reactive Molecular Systems |
title_sort | reducing the cost of neural network potential generation
for reactive molecular systems |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10569056/ https://www.ncbi.nlm.nih.gov/pubmed/37747971 http://dx.doi.org/10.1021/acs.jctc.3c00391 |
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