Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.
Nat Commun. 2022 Jan 10;13(1):68. doi: 10.1038/s41467-021-27627-4.
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that provides 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating realistic coordinates for polymer melt simulations, single-stranded as well as circular single-stranded DNA. We further demonstrate the power of our approach by setting up a microphase-separated block copolymer system, and by generating a liquid-liquid phase separated system inside a lipid vesicle.
分子动力学模拟在（纳米）材料的合理设计和生物大分子的研究中发挥着越来越重要的作用。然而，为这些模拟生成输入文件和现实的起始坐标是一个主要的瓶颈，特别是对于高通量协议和复杂的多组分系统。为了消除这个瓶颈，我们提出了 polyply 软件套件，它提供了 1）一种多尺度图匹配算法，旨在快速生成参数，并且适用于任意复杂的聚合物拓扑结构，2）一种通用的多尺度随机漫步协议，能够高效地建立复杂系统，并且与目标力场或模型分辨率无关。我们通过为聚合物熔体模拟、单链和环状单链 DNA 创建现实的坐标来基准测试方法的质量和性能。我们通过建立一个微相分离嵌段共聚物系统，并在脂质囊泡内生成一个液-液相分离系统，进一步展示了我们方法的强大功能。
