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Simulating a flexible water model as rigid: Best practices and lessons learned
Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model’s Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more stra...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
AIP Publishing LLC
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10076064/ https://www.ncbi.nlm.nih.gov/pubmed/37031157 http://dx.doi.org/10.1063/5.0143836 |
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author | Weldon, Raymond Wang, Feng |
author_facet | Weldon, Raymond Wang, Feng |
author_sort | Weldon, Raymond |
collection | PubMed |
description | Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model’s Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more straightforward to create, it leads to relatively poor performance. The EG model behaves similarly to the corresponding flexible model (the FL model) and, in some cases, agrees even better with experiments. While the difference between the EG and the FL models is mostly a result of flexibility, the MG and EG models have different dipole moments as a result of an effective induction in the condensed phase. For the three water models studied, the property that shows the most difference is the temperature dependence of density. The MG version of the water model by adaptive force matching for ice and liquid does not possess a temperature of maximum density, which is attributed to a downshift of the putative liquid–liquid phase transition line, leading to the hypothesized second critical point of liquid water to manifest at negative pressure. A new three-phase coexistence method for determining the melting temperature of ice is also presented. |
format | Online Article Text |
id | pubmed-10076064 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | AIP Publishing LLC |
record_format | MEDLINE/PubMed |
spelling | pubmed-100760642023-04-06 Simulating a flexible water model as rigid: Best practices and lessons learned Weldon, Raymond Wang, Feng J Chem Phys ARTICLES Two ways to create rigid versions of flexible models are explored. The rigid model can assume the Model’s Geometry (MG) as if the molecule is not interacting with any other molecules or the ensemble averaged geometry (EG) under a particular thermodynamic condition. Although the MG model is more straightforward to create, it leads to relatively poor performance. The EG model behaves similarly to the corresponding flexible model (the FL model) and, in some cases, agrees even better with experiments. While the difference between the EG and the FL models is mostly a result of flexibility, the MG and EG models have different dipole moments as a result of an effective induction in the condensed phase. For the three water models studied, the property that shows the most difference is the temperature dependence of density. The MG version of the water model by adaptive force matching for ice and liquid does not possess a temperature of maximum density, which is attributed to a downshift of the putative liquid–liquid phase transition line, leading to the hypothesized second critical point of liquid water to manifest at negative pressure. A new three-phase coexistence method for determining the melting temperature of ice is also presented. AIP Publishing LLC 2023-04-07 2023-04-03 /pmc/articles/PMC10076064/ /pubmed/37031157 http://dx.doi.org/10.1063/5.0143836 Text en © 2023 Author(s). https://creativecommons.org/licenses/by/4.0/All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ). |
spellingShingle | ARTICLES Weldon, Raymond Wang, Feng Simulating a flexible water model as rigid: Best practices and lessons learned |
title | Simulating a flexible water model as rigid: Best practices and lessons learned |
title_full | Simulating a flexible water model as rigid: Best practices and lessons learned |
title_fullStr | Simulating a flexible water model as rigid: Best practices and lessons learned |
title_full_unstemmed | Simulating a flexible water model as rigid: Best practices and lessons learned |
title_short | Simulating a flexible water model as rigid: Best practices and lessons learned |
title_sort | simulating a flexible water model as rigid: best practices and lessons learned |
topic | ARTICLES |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10076064/ https://www.ncbi.nlm.nih.gov/pubmed/37031157 http://dx.doi.org/10.1063/5.0143836 |
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