Analysis of the SHAKE-SOR algorithm for constrained molecular dynamics simulations

DOI10.4310/MAA.2000.V7.N3.A11MaRDI QIDQ1601150zbMATH OpenOpenAlexFDO

Authors Dexuan Xie, L. Ridgway Scott, Tamar Schlick

Publication date 19 June 2002

Published in Methods and Applications of Analysis (Search for Journal in Brave)

Full work available at URL https://doi.org/10.4310/maa.2000.v7.n3.a11

zbMATH Keywords

SHAKEconstrained molecular dynamicsSOR-Newton iterative method

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Probabilistic models, generic numerical methods in probability and statistics (65C20) Biophysics (92C05)

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Cited in

(11)

• A generalized non-iterative matrix method for constraint molecular dynamics simulations
• A modified shake algorithm for maintaining rigid bonds in molecular dynamics simulations of large molecules
• The Force of Constraint in Predictor-Corrector Algorithms for Shake Constraint Dynamics
• ACCELERATING CONVERGENCE OF MOLECULAR DYNAMICS-BASED STRUCTURAL RELAXATION
• P-SHAKE: a quadratically convergent SHAKE in \(O(n^2)\)
• Trotter derived algorithms for molecular dynamics with constraints: velocity Verlet revisited
• -SHAKE: an extension to SHAKE for the explicit treatment of angular constraints
• Revisiting and parallelizing SHAKE
• WIGGLE: a new constrained molecular dynamics algorithm in Cartesian coordinates
• SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973--1977
• Randomized time Riemannian manifold Hamiltonian Monte Carlo

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