# Molecular Simulation in the Canonical Ensemble and Beyond

ESAIM: Mathematical Modelling and Numerical Analysis (2007)

- Volume: 41, Issue: 2, page 333-350
- ISSN: 0764-583X

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topJia, Zhidong, and Leimkuhler, Ben. "Molecular Simulation in the Canonical Ensemble and Beyond." ESAIM: Mathematical Modelling and Numerical Analysis 41.2 (2007): 333-350. <http://eudml.org/doc/250047>.

@article{Jia2007,

abstract = {
In this paper, we discuss advanced
thermostatting 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 alternative
thermostatting methods, such as Nosé-Poincaré, Nosé-Hoover
(with or without chains), Bulgac-Kusnezov, or recursive Nosé-Poincaré
Chains. These schemes offer possible advantages for use in
computing thermodynamic quantities, and facilitate the development
of multiple time-scale modelling and simulation techniques. In
addition, PTMD advances a preliminary step toward the
realization of true nonequilibrium motion for selected degrees of
freedom, by shielding the variables of interest from the artificial
effect 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.
},

author = {Jia, Zhidong, Leimkuhler, Ben},

journal = {ESAIM: Mathematical Modelling and Numerical Analysis},

keywords = {Molecular dynamics; constant temperature; thermostat; barostat; nonequilibrium simulation.},

language = {eng},

month = {6},

number = {2},

pages = {333-350},

publisher = {EDP Sciences},

title = {Molecular Simulation in the Canonical Ensemble and Beyond},

url = {http://eudml.org/doc/250047},

volume = {41},

year = {2007},

}

TY - JOUR

AU - Jia, Zhidong

AU - Leimkuhler, Ben

TI - Molecular Simulation in the Canonical Ensemble and Beyond

JO - ESAIM: Mathematical Modelling and Numerical Analysis

DA - 2007/6//

PB - EDP Sciences

VL - 41

IS - 2

SP - 333

EP - 350

AB -
In this paper, we discuss advanced
thermostatting 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 alternative
thermostatting methods, such as Nosé-Poincaré, Nosé-Hoover
(with or without chains), Bulgac-Kusnezov, or recursive Nosé-Poincaré
Chains. These schemes offer possible advantages for use in
computing thermodynamic quantities, and facilitate the development
of multiple time-scale modelling and simulation techniques. In
addition, PTMD advances a preliminary step toward the
realization of true nonequilibrium motion for selected degrees of
freedom, by shielding the variables of interest from the artificial
effect 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.

LA - eng

KW - Molecular dynamics; constant temperature; thermostat; barostat; nonequilibrium simulation.

UR - http://eudml.org/doc/250047

ER -

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