A Semi-Analytical Approach to Molecular Dynamics
Journal of Computational Physics 303 (2015) 336–354 Contents lists available at ScienceDirect Journal of Computational Physics www.elsevier.com/locate/jcp A semi-analytical approach to molecular dynamics a,b, c,d Dominik L. Michels ∗, Mathieu Desbrun a Computer Science Department, Stanford University, 353 Serra Mall, MC 9515, Stanford, CA 94305, USA b Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany c Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E. California Blvd., MC 305-16, Pasadena, CA 91125, USA d Centre de Recherche INRIA Sophia-Antipolis Méditerranée, 2004 Route des Lucioles, BP 93, 06902 Sophia Antipolis Cedex, France a r t i c l e i n f o a b s t r a c t Article history: Despite numerous computational advances over the last few decades, molecular dynamics Received 12 July 2014 still favors explicit (and thus easily-parallelizable) time integrators for large scale numerical Received in revised form 28 September simulation. As a consequence, computational efficiency in solving its typically stiff 2015 oscillatory equations of motion is hampered by stringent stability requirements on the Accepted 2 October 2015 time step size. In this paper, we present a semi-analytical integration scheme that offers Available online 13 October 2015 a total speedup of a factor 30 compared to the Verlet method on typical MD simulation Keywords: by allowing over three orders of magnitude larger step sizes. By efficiently approximating Energy conservation the exact integration of the strong (harmonic) forces of covalent bonds through matrix Explicit integration functions, far improved stability with respect to time step size is achieved without Exponential integrators sacrificing the explicit, symplectic, time-reversible, or fine-grained parallelizable nature of Fast Multipole Method the integration scheme.
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