Stochastic-dynamical thermostats for constraints and stiff restraints |
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Authors: | J Bajars J Frank B Leimkuhler |
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Institution: | 1.Centrum Wiskunde & Informatica (CWI),Amsterdam,The Netherlands;2.School of Mathematics and Maxwell Institute for Mathematical Sciences,The University of Edinburgh,Edinburgh,UK |
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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. |
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