Konyukhov Sergei S, Kupchenko Ilya V, Moskovsky Alexander A, Nemukhin Alexander V, Akimov Alexey V, Kolomeisky Anatoly B
Department of Chemistry, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, and N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow 119994, Russian Federation, and Department of Chemistry, Rice University, Houston, Texas 77005.
J Chem Theory Comput. 2010 Sep 14;6(9):2581-90. doi: 10.1021/ct100101y.
Methodical problems of coarse-grained-type molecular dynamics, namely, rigid-body molecular dynamics (RB MD), are studied by investigating the dynamics of nanosized molecular vehicles called nanocars that move on gold and silver surfaces. Specifically, we analyzed the role of thermostats and the effects of temperature, couplings, and correlations between rigid fragments of the nanocar molecule in extensive RB MD simulations. It is found that the use of the Nosé-Poincaré thermostat does not introduce systematic errors, but the time trajectories might be required to be limited to not accumulate large numerical integration errors. Correlations in the motion of different fragments of the molecules are also analyzed. Our theoretical computations also point to the importance of temperature, interfragment interactions, and interactions with surfaces and to the nature of the surface for understanding mechanisms of motion of single-molecule transporters.
通过研究在金和银表面移动的称为纳米车的纳米级分子载体的动力学，对粗粒度型分子动力学，即刚体分子动力学（RB MD）的方法学问题进行了研究。具体而言，我们在广泛的RB MD模拟中分析了恒温器的作用以及纳米车分子刚性片段之间的温度、耦合和相关性的影响。发现使用Nosé-Poincaré恒温器不会引入系统误差，但可能需要限制时间轨迹以避免积累大的数值积分误差。还分析了分子不同片段运动中的相关性。我们的理论计算也指出了温度、片段间相互作用、与表面的相互作用以及表面性质对于理解单分子转运体运动机制的重要性。
