Department of Physical Chemistry, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary.
J Chem Phys. 2012 Aug 7;137(5):054109. doi: 10.1063/1.4739255.
We provide a systematic comparative analysis of various simulation methods for studying steady-state diffusive transport of molecular systems. The methods differ in two respects: (1) the actual method with which the dynamics of the system is handled can be a direct simulation technique [molecular dynamics (MD) and dynamic Monte Carlo (DMC)] or can be an indirect transport equation [the Nernst-Planck (NP) equation], while (2) the driving force of the steady-state transport can be maintained with control cells on the two sides of the transport region [dual control volume (DCV) technique] or it can be maintained in the whole simulation domain with the local equilibrium Monte Carlo (LEMC) technique, where the space is divided into small subvolumes, different chemical potentials are assigned to each, and grand canonical Monte Carlo simulations are performed for them separately. The various combinations of the transport-methods with the driving-force methods have advantages and disadvantages. The MD+DCV and DMC+DCV methods are widely used to study membrane transport. The LEMC method has been introduced with the NP+LEMC technique, which was proved to be a fast, but somewhat empirical method to study diffusion [D. Boda and D. Gillespie, J. Chem. Theor. Comput. 8, 824 (2012)]. In this paper, we introduce the DMC+LEMC method and show that the resulting DMC+LEMC technique has the advantage over the DMC+DCV method that it provides better sampling for the flux, while it has the advantage over the NP+LEMC method that it simulates dynamics directly instead of hiding it in an external adjustable parameter, the diffusion coefficient. The information gained from the DMC+LEMC simulation can be used to construct diffusion coefficient profiles for the NP+LEMC calculations, so a simultaneous application of the two methods is advantageous.
我们提供了一种对研究分子系统稳态扩散输运的各种模拟方法的系统比较分析。这些方法在两个方面有所不同：（1）处理系统动力学的实际方法可以是直接模拟技术[分子动力学（MD）和动态蒙特卡罗（DMC）]，也可以是间接输运方程[能斯特-普朗克（NP）方程]，而（2）稳态输运的驱动力可以通过在输运区域两侧的控制单元[双控制体积（DCV）技术]来维持，也可以通过在整个模拟域中使用局部平衡蒙特卡罗（LEMC）技术来维持，其中空间被划分为小子体积，为每个子体积分配不同的化学势，并对它们分别进行巨正则蒙特卡罗模拟。将输运方法与驱动力方法进行各种组合都有其优缺点。MD+DCV 和 DMC+DCV 方法被广泛用于研究膜运输。LEMC 方法已与 NP+LEMC 技术一起引入，该技术已被证明是一种快速但有些经验的方法，可用于研究扩散[D. Boda 和 D. Gillespie，J. Chem. Theor. Comput. 8, 824（2012）]。在本文中，我们介绍了 DMC+LEMC 方法，并表明所得的 DMC+LEMC 技术相对于 DMC+DCV 方法具有优势，因为它为通量提供了更好的采样，而相对于 NP+LEMC 方法具有优势，因为它直接模拟动力学，而不是将其隐藏在外部可调参数（扩散系数）中。从 DMC+LEMC 模拟中获得的信息可用于为 NP+LEMC 计算构建扩散系数分布，因此同时应用这两种方法是有利的。
