P-SHAKE: a quadratically convergent SHAKE in \(O(n^2)\)
type: Item
instance of: scholarly article
title: P-SHAKE: a quadratically convergent SHAKE in \(O(n^2)\)
zbMATH Open document ID: 1111.82002
author: Pedro Gonnet
published in: Journal of Computational Physics
publication date: 2007-02-19T00:00:00Z
review text: P-SHAKE is a linear constraint solver for rigid and semi-rigid molecules in molecular dynamics simulations and is an extension of the SHAKE algorithm developed in [\textit{J. P. Ryckaert, G. Ciccotti} and \textit{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, 327--341 (1977)]. In the new algorithm the constraint gradients are linearly recombined such that the individual constraint equations become linearly independent. Performances of SHAKE-algorithms are discussed.
reviewed by: Claudia Simionescu-Badea
Mathematics Subject Classification ID: 82-08
zbMATH DE Number: 5128242
zbMATH Keywords: molecular dynamics
zbMATH Keywords: simulations
zbMATH Keywords: constraints
zbMATH Keywords: SHAKE
zbMATH Keywords: M-SHAKE
zbMATH Keywords: Lagrange multipliers
zbMATH Keywords: Newton iteration
zbMATH Keywords: preconditioning
describes a project that uses: SETTLE
describes a project that uses: Maple
describes a project that uses: LINCS
Wikidata QID: Q59567739
MaRDI profile type: Publication
full work available at URL: j.jcp.2006.05.032
OpenAlex ID: W1558157095
cites work: RATTLE: A ''velocity'' version of the SHAKE algorithm for molecular dynamics calculations
cites work: Q4002478
cites work: Q4692387
cites work: Q5185900
cites work: A modified shake algorithm for maintaining rigid bonds in molecular dynamics simulations of large molecules
cites work: WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates
DBLP publication ID: journals/jcphy/Gonnet07
DOI: 10.1016/J.JCP.2006.05.032
description: scientific article; zbMATH DE number 5128242