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

Time Integrators for Molecular Dynamics

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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)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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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