首页 | 中心概况 | 人员构成 | 科学研究 | 学术活动 | 招贤纳士 | 资源下载 | 联系我们 | English Version 
 

J. Chem. Phys. 158, 194301 (2023)

Further cautionary tales on thermostatting in molecular dynamics: Energy equipartitioning and non-equilibrium processes in gas-phase simulations

Roope Halonen 1,*, Ivo Neefjes 2, and Bernhard Reischl 2

1 Center for Joint Quantum Studies and Department of Physics, School of Science, Tianjin University, 92 Weijin Road, Tianjin 300072, China

2 Institute for Atmospheric and Earth System Research/Physics, Faculty of Science, University of Helsinki, P.O. Box 64, Helsinki FI-00014, Finland

* Author to whom correspondence should be addressed: roope@tju.edu.cn

Abstract

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. Here, 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 global (Nosé–Hoover and Canonical Sampling through Velocity Rescaling) and local (Langevin) thermostats for equilibrating a system of flexible compounds and find that of these three only the Langevin thermostat achieves equipartition in a reasonable simulation time. We then study the effect of the unphysical removal of latent heat released during simulations involving multiple dimerization events. As the Langevin thermostat does not produce the correct dynamics in the free molecular regime, we only consider the commonly used Nosé–Hoover thermostat, which is shown to effectively cool down the reactants, leading 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 simulations.

关闭窗口

天津大学理学院 量子交叉研究中心   地址:天津津南区 雅观路135号 天津大学北洋园校区32楼146 
Center for Joint Quantum Studies, School of Science, Tianjin University     Address : Yaguan Road 135, Jinnan District, 300350 Tianjin, P. R. China