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Bayesian selection for coarse-grained models of liquid water
The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions....
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6331618/ https://www.ncbi.nlm.nih.gov/pubmed/30643172 http://dx.doi.org/10.1038/s41598-018-37471-0 |
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author | Zavadlav, Julija Arampatzis, Georgios Koumoutsakos, Petros |
author_facet | Zavadlav, Julija Arampatzis, Georgios Koumoutsakos, Petros |
author_sort | Zavadlav, Julija |
collection | PubMed |
description | The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model’s accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs. |
format | Online Article Text |
id | pubmed-6331618 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-63316182019-01-16 Bayesian selection for coarse-grained models of liquid water Zavadlav, Julija Arampatzis, Georgios Koumoutsakos, Petros Sci Rep Article The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model’s accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs. Nature Publishing Group UK 2019-01-14 /pmc/articles/PMC6331618/ /pubmed/30643172 http://dx.doi.org/10.1038/s41598-018-37471-0 Text en © The Author(s) 2019 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/. |
spellingShingle | Article Zavadlav, Julija Arampatzis, Georgios Koumoutsakos, Petros Bayesian selection for coarse-grained models of liquid water |
title | Bayesian selection for coarse-grained models of liquid water |
title_full | Bayesian selection for coarse-grained models of liquid water |
title_fullStr | Bayesian selection for coarse-grained models of liquid water |
title_full_unstemmed | Bayesian selection for coarse-grained models of liquid water |
title_short | Bayesian selection for coarse-grained models of liquid water |
title_sort | bayesian selection for coarse-grained models of liquid water |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6331618/ https://www.ncbi.nlm.nih.gov/pubmed/30643172 http://dx.doi.org/10.1038/s41598-018-37471-0 |
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