P-SHAKE: A quadratically convergent SHAKE in
Saved in:
| Title: | P-SHAKE: A quadratically convergent SHAKE in |
|---|---|
| Authors: | Gonnet, Pedro1 gonnetp@inf.ethz.ch |
| Source: | Journal of Computational Physics. Jan2007, Vol. 220 Issue 2, p740-750. 11p. |
| Subjects: | Molecular dynamics, Newton-Raphson method, Algorithms, Stochastic convergence |
| Abstract: | Abstract: An algorithm for solving arbitrary linear constraints in molecular dynamics simulations of rigid and semi-rigid molecules is presented. The algorithm – P-SHAKE – is a modified version of the SHAKE [J.-P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes, J. Comput. Phys. 23 (1977) 327–341.] algorithm with a preconditioner applied which effectively de-couples the constraint equations. It achieves quadratic convergence, as does M-SHAKE [V. Kräutler, W.F. van Gunsteren, P.H. Hünenberger, A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. 22 (5) (2001) 501–508.], yet at a cost of only operations per iteration, as opposed to per iteration for M-SHAKE. The algorithm is applied to simulations of rigid water, DMSO, chlorophorm and non-rigid ethane and cyclohexane and is shown to be faster than M-SHAKE by up to a factor of three for relatively small error tolerances. [Copyright &y& Elsevier] |
| Copyright of Journal of Computational Physics is the property of Academic Press Inc. 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 |
|---|---|
| Header | DbId: egs DbLabel: Engineering Source An: 23520828 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: P-SHAKE: A quadratically convergent SHAKE in – 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+Physics%22">Journal of Computational Physics</searchLink>. Jan2007, Vol. 220 Issue 2, p740-750. 11p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Newton-Raphson+method%22">Newton-Raphson method</searchLink><br /><searchLink fieldCode="DE" term="%22Algorithms%22">Algorithms</searchLink><br /><searchLink fieldCode="DE" term="%22Stochastic+convergence%22">Stochastic convergence</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Abstract: An algorithm for solving arbitrary linear constraints in molecular dynamics simulations of rigid and semi-rigid molecules is presented. The algorithm – P-SHAKE – is a modified version of the SHAKE [J.-P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes, J. Comput. Phys. 23 (1977) 327–341.] algorithm with a preconditioner applied which effectively de-couples the constraint equations. It achieves quadratic convergence, as does M-SHAKE [V. Kräutler, W.F. van Gunsteren, P.H. Hünenberger, A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. J. Comput. Chem. 22 (5) (2001) 501–508.], yet at a cost of only operations per iteration, as opposed to per iteration for M-SHAKE. The algorithm is applied to simulations of rigid water, DMSO, chlorophorm and non-rigid ethane and cyclohexane and is shown to be faster than M-SHAKE by up to a factor of three for relatively small error tolerances. [Copyright &y& Elsevier] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Journal of Computational Physics is the property of Academic Press Inc. 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=23520828 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1016/j.jcp.2006.05.032 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 740 Subjects: – SubjectFull: Molecular dynamics Type: general – SubjectFull: Newton-Raphson method Type: general – SubjectFull: Algorithms Type: general – SubjectFull: Stochastic convergence Type: general Titles: – TitleFull: P-SHAKE: A quadratically convergent SHAKE in Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Gonnet, Pedro IsPartOfRelationships: – BibEntity: Dates: – D: 10 M: 01 Text: Jan2007 Type: published Y: 2007 Identifiers: – Type: issn-print Value: 00219991 Numbering: – Type: volume Value: 220 – Type: issue Value: 2 Titles: – TitleFull: Journal of Computational Physics Type: main |
| ResultId | 1 |
