Further cautionary tales on thermostatting in Molecular Dynamics: energy equipartitioning and non-equilibrium processes in gas-phase simulations

Molecular dynamics (MD) simulations of gas-phase chemical reactions are typically carried out on a small number of molecules near thermal equilibrium by means of various thermostatting algorithms. Correct equipartitioning of kinetic energy among translations, rotations and vibrations of the simulated reactants is critical for many processes occurring in the gas phase. As thermalizing collisions are infrequent in gas-phase simulations, the thermostat has to efficiently reach equipartitioning in the system during equilibration and maintain it throughout the actual simulation. Furthermore, in non-equilibrium simulations where heat is released locally, the action of the thermostat should not lead to unphysical changes in the overall dynamics of the system. In this study, we explore issues related to both obtaining and maintaining thermal equilibrium in MD simulations of an exemplary ion-molecule dimerization reaction. We first compare the efficiency of Nosé-Hoover, Canonical Sampling through Velocity Rescaling, and Langevin thermostats for equilibrating the system and find that of these three only the Langevin thermostat achieves equipartition in a reasonable simulation time. We also study the effect of unphysical removal of latent heat released during simulations involving multiple dimerization events, when global thermostatting schemes are applied, which effectively cools down the reactants and leads to an overestimation of the dimerization rate. Our findings underscore the importance of thermostatting for the proper thermal initialization of gas-phase systems and the consequences of global thermostatting in non-equilibrium MD simulations.