Gao Xingyu, Fang Jun, Wang Han
Laboratory of Computational Physics, Huayuan Road 6, Beijing 100088, People's Republic of China.
Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094, People's Republic of China.
J Chem Phys. 2016 Mar 28;144(12):124113. doi: 10.1063/1.4944909.
We present a new method of conducting fully flexible-cell molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way, in the sense that the stationary configurational distribution is proved to be consistent with that of the isothermal-isobaric ensemble. In order to apply the proposed method in computer simulations, a second order symmetric numerical integration scheme is developed by Trotter's splitting of the single-step propagator. Moreover, a practical guide of choosing working parameters is suggested for user specified thermo- and baro-coupling time scales. The method and software implementation are carefully validated by a numerical example.
我们提出了一种基于朗之万运动方程在等温等压系综中进行全柔性细胞分子动力学模拟的新方法。以正确的方式引入了与所有粒子和细胞自由度的随机耦合，即证明稳态构型分布与等温等压系综的分布一致。为了将所提出的方法应用于计算机模拟，通过对单步传播子进行特罗特分裂，开发了一种二阶对称数值积分方案。此外，针对用户指定的热耦合和压耦合时间尺度，给出了选择工作参数的实用指南。通过一个数值例子对该方法和软件实现进行了仔细验证。
