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Critical test of isotropic periodic sum techniques with group-based cut-off schemes

Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every...

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Autores principales: Nozawa, Takuma, Yasuoka, Kenji, Takahashi, Kazuaki Z.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843630/
https://www.ncbi.nlm.nih.gov/pubmed/29520017
http://dx.doi.org/10.1038/s41598-018-22514-3
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author Nozawa, Takuma
Yasuoka, Kenji
Takahashi, Kazuaki Z.
author_facet Nozawa, Takuma
Yasuoka, Kenji
Takahashi, Kazuaki Z.
author_sort Nozawa, Takuma
collection PubMed
description Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of “atoms” inside the cut-off radius, whereas the latter computes interactions of “molecules” inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques.
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spelling pubmed-58436302018-03-14 Critical test of isotropic periodic sum techniques with group-based cut-off schemes Nozawa, Takuma Yasuoka, Kenji Takahashi, Kazuaki Z. Sci Rep Article Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of “atoms” inside the cut-off radius, whereas the latter computes interactions of “molecules” inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques. Nature Publishing Group UK 2018-03-08 /pmc/articles/PMC5843630/ /pubmed/29520017 http://dx.doi.org/10.1038/s41598-018-22514-3 Text en © The Author(s) 2018 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
Nozawa, Takuma
Yasuoka, Kenji
Takahashi, Kazuaki Z.
Critical test of isotropic periodic sum techniques with group-based cut-off schemes
title Critical test of isotropic periodic sum techniques with group-based cut-off schemes
title_full Critical test of isotropic periodic sum techniques with group-based cut-off schemes
title_fullStr Critical test of isotropic periodic sum techniques with group-based cut-off schemes
title_full_unstemmed Critical test of isotropic periodic sum techniques with group-based cut-off schemes
title_short Critical test of isotropic periodic sum techniques with group-based cut-off schemes
title_sort critical test of isotropic periodic sum techniques with group-based cut-off schemes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843630/
https://www.ncbi.nlm.nih.gov/pubmed/29520017
http://dx.doi.org/10.1038/s41598-018-22514-3
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