Time Integrators for Molecular Dynamics

Entropy

关键词: explicit integrators;    Metropolis algorithm;    ergodicity;    weak accuracy;   

DOI  :  10.3390/e16010138

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland