ϑ-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints
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| Title: | ϑ-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints |
|---|---|
| Authors: | Gonnet, Pedro1 gonnetp@inf.ethz.ch, Walther, Jens H.2,3 walther@inf.ethz.ch, Koumoutsakos, Petros2 petros@ethz.ch |
| Source: | Computer Physics Communications. Mar2009, Vol. 180 Issue 3, p360-364. 5p. |
| Subjects: | Algorithm research, Foundations of arithmetic, Constraints (Physics), Molecular dynamics, Dynamics |
| Abstract: | Abstract: This paper presents ϑ-SHAKE, an extension to SHAKE, an algorithm for the resolution of holonomic constraints in molecular dynamics simulations, which allows for the explicit treatment of angular constraints. We show that this treatment is more efficient than the use of fictitious bonds, significantly reducing the overlap between the individual constraints and thus accelerating convergence. The new algorithm is compared with SHAKE, M-SHAKE, the matrix-based approach described by Ciccotti and Ryckaert and P-SHAKE for rigid water and octane. [Copyright &y& Elsevier] |
| Copyright of Computer Physics Communications is the property of Elsevier B.V. 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: 36771619 AccessLevel: 6 PubType: Periodical PubTypeId: serialPeriodical PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: ϑ-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints – 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><br /><searchLink fieldCode="AR" term="%22Walther%2C+Jens+H%2E%22">Walther, Jens H.</searchLink><relatesTo>2,3</relatesTo><i> walther@inf.ethz.ch</i><br /><searchLink fieldCode="AR" term="%22Koumoutsakos%2C+Petros%22">Koumoutsakos, Petros</searchLink><relatesTo>2</relatesTo><i> petros@ethz.ch</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Computer+Physics+Communications%22">Computer Physics Communications</searchLink>. Mar2009, Vol. 180 Issue 3, p360-364. 5p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Algorithm+research%22">Algorithm research</searchLink><br /><searchLink fieldCode="DE" term="%22Foundations+of+arithmetic%22">Foundations of arithmetic</searchLink><br /><searchLink fieldCode="DE" term="%22Constraints+%28Physics%29%22">Constraints (Physics)</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Dynamics%22">Dynamics</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Abstract: This paper presents ϑ-SHAKE, an extension to SHAKE, an algorithm for the resolution of holonomic constraints in molecular dynamics simulations, which allows for the explicit treatment of angular constraints. We show that this treatment is more efficient than the use of fictitious bonds, significantly reducing the overlap between the individual constraints and thus accelerating convergence. The new algorithm is compared with SHAKE, M-SHAKE, the matrix-based approach described by Ciccotti and Ryckaert and P-SHAKE for rigid water and octane. [Copyright &y& Elsevier] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Computer Physics Communications is the property of Elsevier B.V. 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.) |
| PLink | https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=36771619 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.cpc.2008.10.020 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 5 StartPage: 360 Subjects: – SubjectFull: Algorithm research Type: general – SubjectFull: Foundations of arithmetic Type: general – SubjectFull: Constraints (Physics) Type: general – SubjectFull: Molecular dynamics Type: general – SubjectFull: Dynamics Type: general Titles: – TitleFull: ϑ-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Gonnet, Pedro – PersonEntity: Name: NameFull: Walther, Jens H. – PersonEntity: Name: NameFull: Koumoutsakos, Petros IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 03 Text: Mar2009 Type: published Y: 2009 Identifiers: – Type: issn-print Value: 00104655 Numbering: – Type: volume Value: 180 – Type: issue Value: 3 Titles: – TitleFull: Computer Physics Communications Type: main |
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