A semi-analytical approach to molecular dynamics

JOURNAL OF COMPUTATIONAL PHYSICS

卷:303

Article

Michels, Dominik L.^1,2  Desbrun, Mathieu^3,4 

[1] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA

[2] Max Planck Inst Informat, D-66123 Saarbrucken, Germany

[3] CALTECH, Dept Comp & Math Sci, Pasadena, CA 91125 USA

[4] INRIA Sophia Antipolis Mediterranee, Ctr Rech, F-06902 Sophia Antipolis, France

关键词: Energy conservation;    Explicit integration;    Exponential integrators;    Fast Multipole Method;    Krylov subspace projection;    Molecular dynamics;    Momentum conservation;    Symplectic integrators;   

DOI  :  10.1016/j.jcp.2015.10.009

来源: Elsevier

【 摘 要 】

Despite numerous computational advances over the last few decades, molecular dynamics still favors explicit (and thus easily-parallelizable) time integrators for large scale numerical simulation. As a consequence, computational efficiency in solving its typically stiff oscillatory equations of motion is hampered by stringent stability requirements on the time step size. In this paper, we present a semi-analytical integration scheme that offers a total speedup of a factor 30 compared to the Verlet method on typical MD simulation by allowing over three orders of magnitude larger step sizes. By efficiently approximating the exact integration of the strong (harmonic) forces of covalent bonds through matrix functions, far improved stability with respect to time step size is achieved without sacrificing the explicit, symplectic, time-reversible, or fine-grained parallelizable nature of the integration scheme. We demonstrate the efficiency and scalability of our integrator on simulations ranging from DNA strand unbinding and protein folding to nanotube resonators. (C) 2015 Elsevier Inc. All rights reserved.

【 授权许可】

Free