title: Effects of Molecular Dynamics Thermostats on Descriptions of Chemical Nonequilibrium.
abstract: The performance of popular molecular dynamics (MD) thermostat algorithms in constant temperature simulations of equilibrium systems is well-known. This is not the case, however, in the context of nonequilibrium chemical systems, such as chemical reactions or nanoscale self-assembly processes. In this work, we investigate the effect of popular thermostat algorithms on the "natural" (i.e., Hamiltonian) dynamics of a nonequilibrium, chemically reacting system. By comparing constant-temperature quantum mechanical MD (QM/MD) simulations of carbon vapor condensation using velocity scaling, Berendsen, Andersen, Langevin, and Nosé-Hoover chain thermostat algorithms with natural NVE simulations, we show that efficient temperature control and reliable reaction dynamics are mutually exclusive in such a system. This problem may be circumvented, however, by placing the reactive system in an inert He atmosphere, which is itself described using NVT MD. We demonstrate that both realistic temperature control and dynamics consistent with natural NVE dynamics can then be obtained simultaneously. In essence, the thermal energy created by the natural dynamics of the NVE subsystem is drained by the thermostat acting on the NVT atmosphere, without adversely affecting the dynamics of the reactive system itself.
authors.affiliation: Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
authors.forename: Alister J
authors.initials: AJ
authors.lastname: Page
authors.affiliation: Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
authors.forename: Tetsushi
authors.initials: T
authors.lastname: Isomoto
authors.affiliation: Department of Physics, Harvard University, Cambridge, Masachusetts 02138, United States.|Bremen Center for Computational Materials Science - BCCMS, University of Bremen , 28359 Bremen, Germany.
authors.forename: Jan M
authors.initials: JM
authors.lastname: Knaup
authors.affiliation: Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-4602, Japan.
authors.forename: Stephan
authors.initials: S
authors.lastname: Irle
authors.affiliation: Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.|Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States.
authors.forename: Keiji
authors.initials: K
authors.lastname: Morokuma