Time integrators for molecular dynamics

Research output: Contribution to journalArticle

15 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)138-162
Number of pages25
JournalEntropy
Volume16
Issue number1
DOIs
StatePublished - Jan 2014

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)

Keywords

  • Ergodicity
  • Explicit integrators
  • Metropolis algorithm
  • Weak accuracy

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