A Gentle Stochastic Thermostat for Molecular Dynamics View Full Text


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Article Info

DATE

2009-04

AUTHORS

Ben Leimkuhler, Emad Noorizadeh, Florian Theil

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. More... »

PAGES

261-277

References to SciGraph publications

  • 2005. Hypoelliptic Estimates and Spectral Theory for Fokker-Planck Operators and Witten Laplacians in NONE
  • 2007-09. Thermostats for “Slow” Configurational Modes in JOURNAL OF STATISTICAL PHYSICS
  • 1993. Markov Chains and Stochastic Stability in NONE
  • 2007-06. Non-Ergodicity of the Nosé–Hoover Thermostatted Harmonic Oscillator in ARCHIVE FOR RATIONAL MECHANICS AND ANALYSIS
  • 2006. Approach to Thermal Equilibrium in Biomolecular Simulation in NEW ALGORITHMS FOR MACROMOLECULAR SIMULATION
  • 1986. Simplified malliavin calculus in SÉMINAIRE DE PROBABILITÉS XX 1984/85
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10955-009-9734-0

    DOI

    http://dx.doi.org/10.1007/s10955-009-9734-0

    DIMENSIONS

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