Effects of Molecular Dynamics Thermostats on Descriptions of Chemical Nonequilibrium

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 <i>NVE</i> 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 <i>NVT</i> MD. We demonstrate that both realistic temperature control and dynamics consistent with natural <i>NVE</i> dynamics can then be obtained simultaneously. In essence, the thermal energy created by the natural dynamics of the <i>NVE</i> subsystem is drained by the thermostat acting on the <i>NVT</i> atmosphere, without adversely affecting the dynamics of the reactive system itself