Entropy 2014, 16, 138-162; doi:10.3390/e16010138 OPEN ACCESS entropy ISSN 1099-4300 www.mdpi.com/journal/entropy Article Time Integrators for Molecular Dynamics Nawaf Bou-Rabee Department of Mathematical Sciences, Rutgers University—Camden, 311 N 5th Street, Camden, NJ 08102, USA; E-Mail:
[email protected]; Tel.: +1-856-225-6093; Fax: +1-856-225-6602 Received: 19 September 2013; in revised form: 20 November 2013 / Accepted: 4 December 2013 / Published: 27 December 2013 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 MSC Classification: 82C80 (Primary); 82C31, 65C30, 65C05 (Secondary) 1. Introduction Molecular Dynamics (MD) simulation refers to the time integration of Hamilton’s equations often coupled to a heat or pressure bath [1–5]. From its early use in computing equilibrium dynamics of homogeneous molecular systems [6–13] and pico- to nano-scale protein dynamics [14–23], the method has evolved into a general purpose tool for simulating statistical properties of heterogeneous molecular systems [24].