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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...

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Autores principales: Nottoli, Michele, Mikhalev, Aleksandr, Stamm, Benjamin, Lipparini, Filippo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2022
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.
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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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