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Electrostatic Embedding of Machine Learning Potentials
[Image: see text] This work presents a variant of an electrostatic embedding scheme that allows the embedding of arbitrary machine learned potentials trained on molecular systems in vacuo. The scheme is based on physically motivated models of electronic density and polarizability, resulting in a gen...
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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/PMC10061678/ https://www.ncbi.nlm.nih.gov/pubmed/36821513 http://dx.doi.org/10.1021/acs.jctc.2c00914 |
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author | Zinovjev, Kirill |
author_facet | Zinovjev, Kirill |
author_sort | Zinovjev, Kirill |
collection | PubMed |
description | [Image: see text] This work presents a variant of an electrostatic embedding scheme that allows the embedding of arbitrary machine learned potentials trained on molecular systems in vacuo. The scheme is based on physically motivated models of electronic density and polarizability, resulting in a generic model without relying on an exhaustive training set. The scheme only requires in vacuo single point QM calculations to provide training densities and molecular dipolar polarizabilities. As an example, the scheme is applied to create an embedding model for the QM7 data set using Gaussian Process Regression with only 445 reference atomic environments. The model was tested on the SARS-CoV-2 protease complex with PF-00835231, resulting in a predicted embedding energy RMSE of 2 kcal/mol, compared to explicit DFT/MM calculations. |
format | Online Article Text |
id | pubmed-10061678 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-100616782023-03-31 Electrostatic Embedding of Machine Learning Potentials Zinovjev, Kirill J Chem Theory Comput [Image: see text] This work presents a variant of an electrostatic embedding scheme that allows the embedding of arbitrary machine learned potentials trained on molecular systems in vacuo. The scheme is based on physically motivated models of electronic density and polarizability, resulting in a generic model without relying on an exhaustive training set. The scheme only requires in vacuo single point QM calculations to provide training densities and molecular dipolar polarizabilities. As an example, the scheme is applied to create an embedding model for the QM7 data set using Gaussian Process Regression with only 445 reference atomic environments. The model was tested on the SARS-CoV-2 protease complex with PF-00835231, resulting in a predicted embedding energy RMSE of 2 kcal/mol, compared to explicit DFT/MM calculations. American Chemical Society 2023-02-23 /pmc/articles/PMC10061678/ /pubmed/36821513 http://dx.doi.org/10.1021/acs.jctc.2c00914 Text en © 2023 The Author. 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 | Zinovjev, Kirill Electrostatic Embedding of Machine Learning Potentials |
title | Electrostatic Embedding
of Machine Learning Potentials |
title_full | Electrostatic Embedding
of Machine Learning Potentials |
title_fullStr | Electrostatic Embedding
of Machine Learning Potentials |
title_full_unstemmed | Electrostatic Embedding
of Machine Learning Potentials |
title_short | Electrostatic Embedding
of Machine Learning Potentials |
title_sort | electrostatic embedding
of machine learning potentials |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061678/ https://www.ncbi.nlm.nih.gov/pubmed/36821513 http://dx.doi.org/10.1021/acs.jctc.2c00914 |
work_keys_str_mv | AT zinovjevkirill electrostaticembeddingofmachinelearningpotentials |