A Gentle Stochastic Thermostat for Molecular Dynamics

Benedict Leimkuhler, Emad Noorizadeh, Florian Theil

Research output: Contribution to journalArticlepeer-review

Abstract

We discuss a dynamical technique for sampling the canonical measure in molecular dynamics. We present a method that generalizes a recently proposed scheme (Samoletov et al., J. Stat. Phys. 128:1321–1336, 2007), and which controls temperature by use of a device similar to that of Nosé dynamics, but adds random noise to improve ergodicity. In contrast to Langevin dynamics, where noise is added directly to each physical degree of freedom, the new scheme relies on an indirect coupling to a single Brownian particle. For a model with harmonic potentials, we show under a mild non-resonance assumption that we can recover the canonical distribution. In spite of its stochastic nature, experiments suggest that it introduces a relatively weak perturbative effect on the physical dynamics, as measured by perturbation of temporal autocorrelation functions. The kinetic energy is well controlled even in the early stages of a simulation.
Original languageEnglish
Pages (from-to)261-277
JournalJournal of Statistical Physics
Volume135
Issue number2
Early online date8 Apr 2009
DOIs
Publication statusPublished - Apr 2009

Keywords

  • molecular dynamics
  • stochastic thermostats
  • thermodynamic averages
  • Langevin dynamics

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