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A fast and accurate computational method for the linear-combination-based isotropic periodic sum
An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum,...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082916/ https://www.ncbi.nlm.nih.gov/pubmed/30089878 http://dx.doi.org/10.1038/s41598-018-30364-2 |
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author | Takahashi, Kazuaki Z. Nozawa, Takuma Yasuoka, Kenji |
author_facet | Takahashi, Kazuaki Z. Nozawa, Takuma Yasuoka, Kenji |
author_sort | Takahashi, Kazuaki Z. |
collection | PubMed |
description | An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems. |
format | Online Article Text |
id | pubmed-6082916 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-60829162018-08-13 A fast and accurate computational method for the linear-combination-based isotropic periodic sum Takahashi, Kazuaki Z. Nozawa, Takuma Yasuoka, Kenji Sci Rep Article An isotropic periodic sum (IPS) is a powerful technique to reasonably calculate intermolecular interactions for wide range of molecular systems under periodic boundary conditions. A linear-combination-based IPS (LIPS) has been developed to attain computational accuracy close to an exact lattice sum, such as the Ewald sum. The algorithm of the original LIPS method has a high computational cost because it needs long-range interaction calculations in real space. This becomes a performance bottleneck for long-time molecular simulations. In this work, the combination of an LIPS and fast Fourier transform (FFT) was developed, and evaluated on homogeneous and heterogeneous molecular systems. This combinational approach of LIPS/FFT attained computational efficiency close to that of a smooth particle mesh Ewald while maintaining the same high accuracy as the original LIPS. We concluded that LIPS/FFT has great potential to extend the capability of IPS techniques for the fast and accurate computation of many types of molecular systems. Nature Publishing Group UK 2018-08-08 /pmc/articles/PMC6082916/ /pubmed/30089878 http://dx.doi.org/10.1038/s41598-018-30364-2 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 Takahashi, Kazuaki Z. Nozawa, Takuma Yasuoka, Kenji A fast and accurate computational method for the linear-combination-based isotropic periodic sum |
title | A fast and accurate computational method for the linear-combination-based isotropic periodic sum |
title_full | A fast and accurate computational method for the linear-combination-based isotropic periodic sum |
title_fullStr | A fast and accurate computational method for the linear-combination-based isotropic periodic sum |
title_full_unstemmed | A fast and accurate computational method for the linear-combination-based isotropic periodic sum |
title_short | A fast and accurate computational method for the linear-combination-based isotropic periodic sum |
title_sort | fast and accurate computational method for the linear-combination-based isotropic periodic sum |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082916/ https://www.ncbi.nlm.nih.gov/pubmed/30089878 http://dx.doi.org/10.1038/s41598-018-30364-2 |
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