Cargando…
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...
Autores principales: | , , |
---|---|
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 |
_version_ | 1783305104471883776 |
---|---|
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. |
format | Online Article Text |
id | pubmed-5843630 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT nozawatakuma criticaltestofisotropicperiodicsumtechniqueswithgroupbasedcutoffschemes AT yasuokakenji criticaltestofisotropicperiodicsumtechniqueswithgroupbasedcutoffschemes AT takahashikazuakiz criticaltestofisotropicperiodicsumtechniqueswithgroupbasedcutoffschemes |