Cargando…
Data-driven analysis of the number of Lennard–Jones types needed in a force field
Force fields used in molecular simulations contain numerical parameters, such as Lennard–Jones (LJ) parameters, which are assigned to the atoms in a molecule based on a classification of their chemical environments. The number of classes, or types, should be no more than needed to maximize agreement...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8294475/ https://www.ncbi.nlm.nih.gov/pubmed/34295996 http://dx.doi.org/10.1038/s42004-020-00395-w |
_version_ | 1783725242054606848 |
---|---|
author | Schauperl, Michael Kantonen, Sophie M Wang, Lee-Ping Gilson, Michael K |
author_facet | Schauperl, Michael Kantonen, Sophie M Wang, Lee-Ping Gilson, Michael K |
author_sort | Schauperl, Michael |
collection | PubMed |
description | Force fields used in molecular simulations contain numerical parameters, such as Lennard–Jones (LJ) parameters, which are assigned to the atoms in a molecule based on a classification of their chemical environments. The number of classes, or types, should be no more than needed to maximize agreement with experiment, as parsimony avoids overfitting and simplifies parameter optimization. However, types have historically been crafted based largely on chemical intuition, so current force fields may contain more types than needed. In this study, we seek the minimum number of LJ parameter types needed to represent the key properties of organic liquids. We find that highly competitive force field accuracy is obtained with minimalist sets of LJ types; e.g., two H types and one type apiece for C, O, and N atoms. We also find that the fitness surface has multiple minima, which can lead to local trapping of the optimizer. |
format | Online Article Text |
id | pubmed-8294475 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-82944752021-07-21 Data-driven analysis of the number of Lennard–Jones types needed in a force field Schauperl, Michael Kantonen, Sophie M Wang, Lee-Ping Gilson, Michael K Commun Chem Article Force fields used in molecular simulations contain numerical parameters, such as Lennard–Jones (LJ) parameters, which are assigned to the atoms in a molecule based on a classification of their chemical environments. The number of classes, or types, should be no more than needed to maximize agreement with experiment, as parsimony avoids overfitting and simplifies parameter optimization. However, types have historically been crafted based largely on chemical intuition, so current force fields may contain more types than needed. In this study, we seek the minimum number of LJ parameter types needed to represent the key properties of organic liquids. We find that highly competitive force field accuracy is obtained with minimalist sets of LJ types; e.g., two H types and one type apiece for C, O, and N atoms. We also find that the fitness surface has multiple minima, which can lead to local trapping of the optimizer. Nature Publishing Group UK 2020-11-13 /pmc/articles/PMC8294475/ /pubmed/34295996 http://dx.doi.org/10.1038/s42004-020-00395-w Text en © The Author(s) 2020 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Schauperl, Michael Kantonen, Sophie M Wang, Lee-Ping Gilson, Michael K Data-driven analysis of the number of Lennard–Jones types needed in a force field |
title | Data-driven analysis of the number of Lennard–Jones types needed in a force field |
title_full | Data-driven analysis of the number of Lennard–Jones types needed in a force field |
title_fullStr | Data-driven analysis of the number of Lennard–Jones types needed in a force field |
title_full_unstemmed | Data-driven analysis of the number of Lennard–Jones types needed in a force field |
title_short | Data-driven analysis of the number of Lennard–Jones types needed in a force field |
title_sort | data-driven analysis of the number of lennard–jones types needed in a force field |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8294475/ https://www.ncbi.nlm.nih.gov/pubmed/34295996 http://dx.doi.org/10.1038/s42004-020-00395-w |
work_keys_str_mv | AT schauperlmichael datadrivenanalysisofthenumberoflennardjonestypesneededinaforcefield AT kantonensophiem datadrivenanalysisofthenumberoflennardjonestypesneededinaforcefield AT wangleeping datadrivenanalysisofthenumberoflennardjonestypesneededinaforcefield AT gilsonmichaelk datadrivenanalysisofthenumberoflennardjonestypesneededinaforcefield |