Barsky Sandra, Delgado-Buscalioni Rafael, Coveney Peter V
Centre for Computational Science, Department of Chemistry, University College London, WC1H 0AJ, UK.
J Chem Phys. 2004 Aug 1;121(5):2403-11. doi: 10.1063/1.1767996.
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport information from the other two domains is exchanged. The exchange of information in the overlap region ensures that momentum, energy, and mass are conserved. The validity of the hybrid code is demonstrated by studying a single polymer tethered to a hard wall immersed in explicit solvent and undergoing shear flow. In classical molecular dynamics simulation a great deal of computational time is devoted to simulating solvent molecules, although the solvent itself is of no direct interest. By contrast, the hybrid code simulates the polymer and surrounding solvent explicitly, whereas the solvent farther away from the polymer is modeled using a continuum description. In the hybrid simulations the MD domain is an open system whose number of particles is controlled to filter the perturbative density waves produced by the polymer motion. We compare conformational properties of the polymer in both simulations for various shear rates. In all cases polymer properties compare extremely well between the two simulation scenarios, thereby demonstrating that this hybrid method is a useful way to model a system with polymers and under nonzero flow conditions. There is also good agreement between the MD and hybrid schemes and experimental data on tethered DNA in flow. The computational cost of the hybrid protocol can be reduced to less than 6% of the cost of updating the MD forces, confirming the practical value of the method.
我们将一种新开发的结合经典分子动力学（MD）和计算流体动力学（CFD）的混合模拟方法与仅由分子动力学组成的模拟进行比较。混合代码由三个区域组成：一个经典MD区域、一个通过标准CFD方法求解动力学方程的连续介质域，以及一个交换来自其他两个域的传输信息的重叠域。重叠区域中的信息交换确保动量、能量和质量守恒。通过研究一个 tethered 到浸没在显式溶剂中的硬壁上并经历剪切流的单个聚合物，证明了混合代码的有效性。在经典分子动力学模拟中，大量计算时间用于模拟溶剂分子，尽管溶剂本身并非直接关注对象。相比之下，混合代码显式模拟聚合物和周围溶剂，而远离聚合物的溶剂则使用连续介质描述进行建模。在混合模拟中，MD域是一个开放系统，其粒子数量受到控制，以过滤由聚合物运动产生的微扰密度波。我们比较了两种模拟中聚合物在不同剪切速率下的构象性质。在所有情况下，两种模拟场景下的聚合物性质都非常吻合，从而证明这种混合方法是在非零流动条件下对含有聚合物的系统进行建模的一种有用方式。MD和混合方案与流动中 tethered DNA 的实验数据之间也有很好的一致性。混合协议的计算成本可以降低到更新MD力成本的6%以下，证实了该方法的实用价值。
