Effects of Molecular Dynamics Thermostats on Descriptions of Chemical Nonequilibrium.
Effects of Molecular Dynamics Thermostats on Descriptions of Chemical Nonequilibrium.
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DOI：
10.1021/ct3004639
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发表时间：
2012-10
影响因子：
5.5
通讯作者：
A. Page;Tetsushi Isomoto;J. Knaup;S. Irle;K. Morokuma
中科院分区：
文献类型：
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作者：
A. Page;Tetsushi Isomoto;J. Knaup;S. Irle;K. Morokuma
常用的分子动力学（MD）恒温器算法在平衡体系恒温模拟中的性能是众所周知的。然而，在非平衡化学系统的背景下，例如化学反应或纳米级自组装过程，情况并非如此。在这项工作中，我们研究了流行的恒温器算法对“自然”（即，非平衡化学反应系统的动力学。通过比较恒温量子力学分子动力学（QM/MD）模拟碳蒸汽冷凝速度标度，Berendsen，Andersen，Langevin和Nosé-Hoover链恒温器算法与自然NVE模拟，我们表明，有效的温度控制和可靠的反应动力学是相互排斥的，在这样的系统。然而，这个问题可以通过将反应系统置于惰性He气氛中来规避，惰性He气氛本身使用NVT MD来描述。我们证明，现实的温度控制和动态符合自然NVE动态，然后可以同时获得。本质上，由NVE子系统的自然动态产生的热能由作用于NVT气氛的恒温器排出，而不会不利地影响反应系统本身的动态。
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.