The European Physical Journal Special Topics

, Volume 200, Issue 1, pp 131–152

Stochastic-dynamical thermostats for constraints and stiff restraints

Regular Article

DOI: 10.1140/epjst/e2011-01522-0

Cite this article as:
Bajars, J., Frank, J. & Leimkuhler, B. Eur. Phys. J. Spec. Top. (2011) 200: 131. doi:10.1140/epjst/e2011-01522-0

Abstract

A broad array of canonical sampling methods are available for molecular simulation based on stochastic-dynamical perturbation of Newtonian dynamics, including Langevin dynamics, Stochastic Velo- city Rescaling, and methods that combine Nosé-Hoover dynamics with stochastic perturbation. In this article we discuss several stochastic-dynamical thermostats in the setting of simulating systems with holonomic constraints. The approaches described are easily implemented and facilitate the recovery of correct canonical averages with minimal disturbance of the underlying dynamics. For the purpose of illustrating our results, we examine the numerical application of these methods to a simple atomic chain, where a Fixman term is required to correct the thermodynamic ensemble.

Copyright information

© EDP Sciences and Springer 2011

Authors and Affiliations

  1. 1.Centrum Wiskunde & Informatica (CWI)AmsterdamThe Netherlands
  2. 2.School of Mathematics and Maxwell Institute for Mathematical SciencesThe University of EdinburghEdinburghUK

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