Increasing the Time Step and Efficiency of Molecular Dynamics Simulations: Optimal Solutions for Equilibrium Simulations or Structure Refinement of Large Biomolecules

DOI10.1080/0892702031000065791zbMath1015.92007OpenAlexW1965159558MaRDI QIDQ4803162

Daniel Juchli, Wilfred F. van Gunsteren, Urs Stocker

Publication date: 15 July 2003

Published in: Molecular Simulation (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1080/0892702031000065791

zbMATH Keywords

equations of motionconstraintsmolecular dynamics simulationbiomoleculestime steps

Mathematics Subject Classification ID

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

Uses Software

• GROMOS

Cites Work

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• Derivation and testing of explicit equations of motion for polymers described by internal coordinates
• Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of Störmer-Leapfrog integrators
• A fast recursive algorithm for molecular dynamics simulation
• Smoothed dynamics of highly oscillatory Hamiltonian systems
• Rotational Dynamics of large molecules

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