Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics

DOI10.1006/JCPH.1999.6202zbMath0977.92012OpenAlexW2111906305MaRDI QIDQ1305947

Adrian Sandu, Tamar Schlick

Publication date: 22 January 2002

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

Full work available at URL: https://semanticscholar.org/paper/085b9f4acf39571f0529e773718e590c019198c3

zbMATH Keywords

force splittingsymplecticnessbiomolecular dynamics simulationsmultiple timestepsnumerical resonance

Mathematics Subject Classification ID

Probabilistic models, generic numerical methods in probability and statistics (65C20) Dynamical systems in biology (37N25) Biochemistry, molecular biology (92C40)

Related Items (3)

Stability of asynchronous variational integrators ⋮ Error and timing analysis of multiple time-step integration methods for molecular dynamics ⋮ Algorithmic challenges in computational molecular biophysics

Uses Software

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• CHARMM

Cites Work

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• A multiple time-step method for molecular dynamics simulations of fluids of chain molecules
• Algorithmic challenges in computational molecular biophysics
• Effective computational strategies for determining structures of carcinogen-damaged DNA
• Dangers of multiple time step methods
• Nonlinear resonance artifacts in molecular dynamics simulations
• A Family of Symplectic Integrators: Stability, Accuracy, and Molecular Dynamics Applications
• TNPACK—A truncated Newton minimization package for large-scale problems
• TNPACK—a truncated Newton minimization package for large-scale problems
• Efficient Implementation of the Truncated-Newton Algorithm for Large-Scale Chemistry Applications

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