A Semi-analytical Approach to Molecular Dynamics

Dominik L. Michels,Stanford University,
Mathieu Desbrun,California Institute of Technology.
In Journal of Computational Physics, Volume 303, Pages 336-354, Elsevier, Dec. 2015.


author = {Dominik L.~Michels and Mathieu Desbrun},
title = {A Semi-analytical Approach to Molecular Dynamics},
journal = {J.~Comput.~Phys.},
volume = {303},
number = {},
pages = {336--354},
year = {2015},
month = dec,
publisher = {Elsevier},
address = {Amsterdam}


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.

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