Nonlinear resonance artifacts in molecular dynamics simulations

DOI10.1006/jcph.1998.5879zbMath0905.65084OpenAlexW2023305549MaRDI QIDQ1387887

D. Massart

Publication date: 3 August 1998

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

Full work available at URL: https://semanticscholar.org/paper/88e33bae3afda1c4f718fdaa5bf2c7729b615c3e

zbMATH Keywords

numerical experimentsequation of motionmolecular dynamicstime integratorsimplicit symplectic schemesspurious resonance

Mathematics Subject Classification ID

Numerical methods for initial value problems involving ordinary differential equations (65L05) Molecular physics (81V55) Dynamical systems and ergodic theory (37-XX)

Related Items

A Filon-type asymptotic approach to solving highly oscillatory second-order initial value problems, Improved filon-type asymptotic methods for highly oscillatory differential equations with multiple time scales, Cheap implicit symplectic integrators, Adaptive multi-stage integrators for optimal energy conservation in molecular simulations, Thread-Parallel Anisotropic Mesh Adaptation, A fast mollified impulse method for biomolecular atomistic simulations, The effects of intrinsic dynamical ghost modes in discrete-time Langevin simulations, Stability of asynchronous variational integrators, Efficient energy-preserving integrators for oscillatory Hamiltonian systems, A unified operator splitting approach for multi-scale fluid-particle coupling in the lattice Boltzmann method, Underresolved simulations of heat baths, A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma, Symplectic integration with floating-point arithmetic and other approximations, Algorithmic challenges in computational molecular biophysics, Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics

Uses Software

• TNPACK

Cites Work

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• The discrete energy-momentum method. Conserving algorithms for nonlinear elastodynamics
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• Cheap implicit symplectic integrators
• A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications
• The accuracy of symplectic integrators
• TNPACK—A truncated Newton minimization package for large-scale problems
• Molecular dynamics by the Backward‐Euler method