A generalized non-iterative matrix method for constraint molecular dynamics simulations

DOI10.1006/JCPH.2001.6819MaRDI QIDQ5951843zbMATH OpenOpenAlexFDO

Authors Makoto Yoneya

Publication date 25 April 2002

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

Full work available at URL https://doi.org/10.1006/jcph.2001.6819

zbMATH Keywords

bond lengthSHAKEVerlet method

Mathematics Subject Classification ID

Simulation of dynamical systems (37M05) Computational methods for problems pertaining to quantum theory (81-08) Molecular physics (81V55)

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Cites work

• Explicit Canonical Methods for Hamiltonian Systems
• scientific article; zbMATH DE number 1082719 (Why is no real title available?)
• Non-Iterative Constraint Dynamics Using Velocity-Explicit Verlet Methods
• Symplectic numerical integrators in constrained Hamiltonian systems

Cited in

(14)

• Objective molecular dynamics
• Compensating mass matrix potential for constrained molecular dynamics
• Parallel constrained molecular dynamics
• Analysis of the SHAKE-SOR algorithm for constrained molecular dynamics simulations
• New approaches for molecular dynamics simulations with nonholonomic constraints
• Constrained molecular dynamics. II: An \(N\)-body approach to nuclear systems
• A GENERALIZED CELL METHOD FOR HARD DISK MOLECULAR DYNAMICS SIMULATION OF POLYDISPERSE SYSTEMS
• 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
• Internal coordinate molecular dynamics based on the spectroscopic B-matrix
• Heuristic computation of the rovibrational \(\mathbf {G}\) matrix in optimized molecule-fixed axes. \texttt{Gmat 2.1}
• A simulation method of combinding boundary element method with generalized Langevin dynamics
• GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates

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• LINCS

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