Common molecular dynamics algorithms revisited: Accuracy and optimal time steps of Störmer-Leapfrog integrators

DOI10.1006/JCPH.1997.5740MaRDI QIDQ1371996zbMATH OpenOpenAlexFDO

Authors Alexey K. Mazur

Publication date 15 December 1997

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

Full work available at URL https://arxiv.org/abs/physics/9707008

zbMATH Keywords

numerical testsmolecular dynamics algorithmsStörmer-Verlet-leapfrog integrators

Mathematics Subject Classification ID

PDEs in connection with quantum mechanics (35Q40) Molecular physics (81V55) Applications to the sciences (65Z05)

Abstract: The Stoermer-Verlet-leapfrog group of integrators commonly used in molecular dynamics simulations has long become a textbook subject and seems to have been studied exhaustively. There are, however, a few striking effects in performance of algorithms which are well-known but have not received adequate attention in the literature. A closer view of these unclear observations results in unexpected conclusions. It is shown here that contrary to the conventional point of view, the leapfrog scheme is distinguished in this group both in terms of the order of truncation errors and the conservation of the total energy. In this case the characteristic square growth of fluctuations of the total energy with the step size, commonly measured in numerical tests, results from additional interpolation errors with no relation to the accuracy of the computed trajectory. An alternative procedure is described for checking energy conservation of leapfrog-like algorithms which is free from interpolation errors. Preliminary tests on a representative model system suggest that standard step size values used at present are lower than necessary for accurate sampling.

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Cites work

• scientific article; zbMATH DE number 41859 (Why is no real title available?)
• scientific article; zbMATH DE number 46777 (Why is no real title available?)
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Cited in

(12)

• Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
• An implicit particle-in-cell method for granular materials
• Comparison of effective and stable Langevin dynamics integrators
• An arbitrary order time-stepping algorithm for tracking particles in inhomogeneous magnetic fields
• Increasing the Time Step and Efficiency of Molecular Dynamics Simulations: Optimal Solutions for Equilibrium Simulations or Structure Refinement of Large Biomolecules
• New applications for the Boris Spectral Deferred Correction algorithm for plasma simulations
• New integrator for molecular dynamics simulations
• Trajectory integration with potential energy discontinuities
• Adaptive multi-stage integration schemes for Hamiltonian Monte Carlo
• Adding an energy-like conservation law to the leapfrog integrator
• A New Leapfrog Integrator of Rotational Motion. The Revised Angular-Momentum Approach
• Error and timing analysis of multiple time-step integration methods for molecular dynamics

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