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Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library
[Image: see text] The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9639080/ https://www.ncbi.nlm.nih.gov/pubmed/36265187 http://dx.doi.org/10.1021/acs.jpcb.2c04579 |
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author | Nottoli, Michele Mikhalev, Aleksandr Stamm, Benjamin Lipparini, Filippo |
author_facet | Nottoli, Michele Mikhalev, Aleksandr Stamm, Benjamin Lipparini, Filippo |
author_sort | Nottoli, Michele |
collection | PubMed |
description | [Image: see text] The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The interface was used to test a united atom coarse-graining strategy that allowed us to push ddCOSMO to its limits by computing solvation energies on systems with up to 7 million atoms. We first present benchmarks to find an optimal discretization, and then, we discuss the performance and results obtained with fine- and coarse-grained solvation energy calculations. |
format | Online Article Text |
id | pubmed-9639080 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-96390802022-11-08 Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library Nottoli, Michele Mikhalev, Aleksandr Stamm, Benjamin Lipparini, Filippo J Phys Chem B [Image: see text] The domain decomposition conductor-like screening model is an efficient way to compute the solvation energy of solutes within a polarizable continuum medium in a linear scaling computational time. Despite its efficiency, the application to very large systems is still challenging. A possibility to further accelerate the algorithm is resorting to coarse-graining strategies. In this paper we present a preliminary interface between the molecular dynamics package Tinker and the ddX library. The interface was used to test a united atom coarse-graining strategy that allowed us to push ddCOSMO to its limits by computing solvation energies on systems with up to 7 million atoms. We first present benchmarks to find an optimal discretization, and then, we discuss the performance and results obtained with fine- and coarse-grained solvation energy calculations. American Chemical Society 2022-10-20 2022-11-03 /pmc/articles/PMC9639080/ /pubmed/36265187 http://dx.doi.org/10.1021/acs.jpcb.2c04579 Text en © 2022 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 | Nottoli, Michele Mikhalev, Aleksandr Stamm, Benjamin Lipparini, Filippo Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library |
title | Coarse-Graining
ddCOSMO through an Interface between
Tinker and the ddX Library |
title_full | Coarse-Graining
ddCOSMO through an Interface between
Tinker and the ddX Library |
title_fullStr | Coarse-Graining
ddCOSMO through an Interface between
Tinker and the ddX Library |
title_full_unstemmed | Coarse-Graining
ddCOSMO through an Interface between
Tinker and the ddX Library |
title_short | Coarse-Graining
ddCOSMO through an Interface between
Tinker and the ddX Library |
title_sort | coarse-graining
ddcosmo through an interface between
tinker and the ddx library |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9639080/ https://www.ncbi.nlm.nih.gov/pubmed/36265187 http://dx.doi.org/10.1021/acs.jpcb.2c04579 |
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