Entropy 2014, 16(1), 138-162; doi:10.3390/e16010138

Time Integrators for Molecular Dynamics

Department of Mathematical Sciences, Rutgers University—Camden, 311 N 5th Street, Camden, NJ 08102, USA
Received: 19 September 2013; in revised form: 20 November 2013 / Accepted: 4 December 2013 / Published: 27 December 2013
(This article belongs to the Special Issue Molecular Dynamics Simulation)
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Abstract: This paper invites the reader to learn more about time integrators for Molecular Dynamics simulation through a simple MATLAB implementation. An overview of methods is provided from an algorithmic viewpoint that emphasizes long-time stability and finite-time dynamic accuracy. The given software simulates Langevin dynamics using an explicit, second-order (weakly) accurate integrator that exactly reproduces the Boltzmann-Gibbs density. This latter feature comes from adding a Metropolis acceptance-rejection step to the integrator. The paper discusses in detail the properties of the integrator. Since these properties do not rely on a specific form of a heat or pressure bath model, the given algorithm can be used to simulate other bath models including, e.g., the widely used v-rescale thermostat.
Keywords: explicit integrators; Metropolis algorithm; ergodicity; weak accuracy

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MDPI and ACS Style

Bou-Rabee, N. Time Integrators for Molecular Dynamics. Entropy 2014, 16, 138-162.

AMA Style

Bou-Rabee N. Time Integrators for Molecular Dynamics. Entropy. 2014; 16(1):138-162.

Chicago/Turabian Style

Bou-Rabee, Nawaf. 2014. "Time Integrators for Molecular Dynamics." Entropy 16, no. 1: 138-162.

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