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Molecular Simulation in the Canonical Ensemble and Beyond

Published online by Cambridge University Press:  16 June 2007

Zhidong Jia  and
Ben Leimkuhler
Zhidong Jia
Affiliation:
ICMSEC, P.O. Box 2719, Beijing 100080, China.
Ben Leimkuhler
Affiliation:
School of Mathematics and Maxwell Institute, University of Edinburgh, Edinburgh EH9 3JZ, UK.
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Abstract

In this paper, we discuss advancedthermostatting techniques for sampling molecular systems in the canonical ensemble.We first survey work on dynamical thermostatting methods, including the Nosé-Poincaré method, and generalized bath methods which introduce a more complicated extended model to obtain better ergodicity. We describe a general controlled temperature model, projective thermostatting molecular dynamics(PTMD) and demonstrate that it flexibly accommodates existing alternativethermostatting methods, such as Nosé-Poincaré, Nosé-Hoover(with or without chains), Bulgac-Kusnezov, or recursive Nosé-PoincaréChains. These schemes offer possible advantages for use incomputing thermodynamic quantities, and facilitate the developmentof multiple time-scale modelling and simulation techniques. Inaddition, PTMD advances a preliminary step toward therealization of true nonequilibrium motion for selected degrees offreedom, by shielding the variables of interest from the artificialeffect of thermostats. We discuss extension of the PTMD method for constant temperature and pressure models. Finally, we demonstrate schemes for simulating systems with an artificial temperature gradient, by enabling the use of two temperature baths within the PTMD framework.

Keywords

Molecular dynamicsconstant temperaturethermostatbarostatnonequilibrium simulation.
Type
Research Article
Information
ESAIM: Mathematical Modelling and Numerical Analysis , Volume 41 , Issue 2: Special issue on Molecular Modelling , March 2007 , pp. 333 - 350
Copyright
© EDP Sciences, SMAI, 2007

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