A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations.
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| Title: | A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations. |
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| Authors: | Gonnet, Pedro1 gonnetp@inf.ethz.ch |
| Source: | Journal of Computational Chemistry. 2007, Vol. 28 Issue 2, p570-573. 4p. 3 Diagrams, 1 Chart. |
| Subjects: | Molecular dynamics, Particles, Mechanics (Physics), Algorithms, Cells |
| Abstract: | Cell lists are ubiquitous in molecular dynamics simulations—be it for the direct computation of short-range inter-atomic potentials, the short-range direct part of a long-range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary interparticle distance calculations. In this paper, an algorithm is presented which reduces the number of spurious distance calculations by first sorting the particles along the cell pair axis and then only interacting two particles if their distance along the axis is smaller than the cutoff distance of the interaction. This approach is shown to be more efficient than the conventional approach and similar approaches using smaller cells. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 570–573, 2007 [ABSTRACT FROM AUTHOR] |
| Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 23527418 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Gonnet%2C+Pedro%22">Gonnet, Pedro</searchLink><relatesTo>1</relatesTo><i> gonnetp@inf.ethz.ch</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Journal+of+Computational+Chemistry%22">Journal of Computational Chemistry</searchLink>. 2007, Vol. 28 Issue 2, p570-573. 4p. 3 Diagrams, 1 Chart. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Particles%22">Particles</searchLink><br /><searchLink fieldCode="DE" term="%22Mechanics+%28Physics%29%22">Mechanics (Physics)</searchLink><br /><searchLink fieldCode="DE" term="%22Algorithms%22">Algorithms</searchLink><br /><searchLink fieldCode="DE" term="%22Cells%22">Cells</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Cell lists are ubiquitous in molecular dynamics simulations—be it for the direct computation of short-range inter-atomic potentials, the short-range direct part of a long-range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary interparticle distance calculations. In this paper, an algorithm is presented which reduces the number of spurious distance calculations by first sorting the particles along the cell pair axis and then only interacting two particles if their distance along the axis is smaller than the cutoff distance of the interaction. This approach is shown to be more efficient than the conventional approach and similar approaches using smaller cells. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 570–573, 2007 [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1002/jcc.20563 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 4 StartPage: 570 Subjects: – SubjectFull: Molecular dynamics Type: general – SubjectFull: Particles Type: general – SubjectFull: Mechanics (Physics) Type: general – SubjectFull: Algorithms Type: general – SubjectFull: Cells Type: general Titles: – TitleFull: A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Gonnet, Pedro IsPartOfRelationships: – BibEntity: Dates: – D: 30 M: 01 Text: 2007 Type: published Y: 2007 Identifiers: – Type: issn-print Value: 01928651 Numbering: – Type: volume Value: 28 – Type: issue Value: 2 Titles: – TitleFull: Journal of Computational Chemistry Type: main |
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