Chair of Computational Science, ETH Zürich, Clausiusstrasse 33, CH-8092 Zurich, Switzerland.
Department of Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
J Chem Phys. 2017 Sep 21;147(11):114110. doi: 10.1063/1.4986916.
Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.
多尺度方法是解决软物质和分子液体中遇到的时空尺度相互关联的最有效方法。在文献中,报道的混合方法从量子到原子、粗粒和连续体长度尺度都有涉及。在本文中,我们提出了分子动力学(MD)和耗散粒子动力学(DPD)方法的混合耦合,从而连接微观和介观描述。界面是在自适应分辨率方案(AdResS)中进行的,这是一种线性动量守恒的耦合技术。我们的方法适用于模拟在微/介观尺度下的流体,其中流体动力学起着重要作用。所提出的方法在环境条件下的水进行了展示。超分子耦合是通过最近开发的聚类算法 SWINGER 实现的,该算法在模拟过程中根据需要组装、拆卸和重新组装簇。这允许在标准原子 MD 和 DPD 模型之间进行无缝耦合。所开发的框架可以很容易地应用于材料和生命科学领域的各种应用,例如磷脂和聚合物熔体的模拟,或研究正常和疾病状态下的红细胞行为。