P-SHAKE: a quadratically convergent SHAKE in O(n^2)

DOI10.1016/J.JCP.2006.05.032MaRDI QIDQ868237zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Pedro Gonnet

Publication date 19 February 2007

Published in Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jcp.2006.05.032

zbMATH Keywords

constraintsLagrange multipliersM-SHAKEmolecular dynamicsNewton iterationpreconditioningSHAKEsimulations

Mathematics Subject Classification ID

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.

Recommendations

• Revisiting and parallelizing SHAKE
• New approaches for molecular dynamics simulations with nonholonomic constraints
• Analysis of the SHAKE-SOR algorithm for constrained molecular dynamics simulations
• The Force of Constraint in Predictor-Corrector Algorithms for Shake Constraint Dynamics
• Efficient constraint dynamics using MILC SHAKE

Cites work

• A modified shake algorithm for maintaining rigid bonds in molecular dynamics simulations of large molecules
• scientific article; zbMATH DE number 52125 (Why is no real title available?)
• scientific article; zbMATH DE number 194432 (Why is no real title available?)
• scientific article; zbMATH DE number 3892457 (Why is no real title available?)
• RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
• WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates

Cited in

(14)

• A modified shake algorithm for maintaining rigid bonds in molecular dynamics simulations of large molecules
• Parallel constrained molecular dynamics
• Analysis of the SHAKE-SOR algorithm for constrained molecular dynamics simulations
• New approaches for molecular dynamics simulations with nonholonomic constraints
• Revisiting and parallelizing SHAKE
• WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates
• ACCELERATING CONVERGENCE OF MOLECULAR DYNAMICS-BASED STRUCTURAL RELAXATION
• The Force of Constraint in Predictor-Corrector Algorithms for Shake Constraint Dynamics
• Non-Iterative Constraint Dynamics Using Velocity-Explicit Verlet Methods
• A penalty function method for constrained molecular dynamics simulation
• -SHAKE: an extension to SHAKE for the explicit treatment of angular constraints
• Trotter derived algorithms for molecular dynamics with constraints: velocity Verlet revisited
• A technique for calculating particle systems containing rigid and soft parts
• Efficient constraint dynamics using MILC SHAKE

Describes a project that uses

Uses Software

• SETTLE
• Maple
• LINCS

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