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Abstract：
Soft condensed matter is challenging to study due to the vast time and length scales that are necessary to accurately represent complex systems and capture their underlying physics. Multiscale simulations are necessary to study processes that have disparate time and/or length scales, which abound throughout biology and other complex systems. Herein we present ezAlign, an open-source software for converting coarse-grained molecular dynamics structures to atomistic representation, allowing multiscale modeling of biomolecular systems. The ezAlign v1.1 software package is publicly available for download at github.com/LLNL/ezAlign. Its underlying methodology is based on a simple alignment of an atomistic template molecule, followed by position-restraint energy minimization, which forces the atomistic molecule to adopt a conformation consistent with the coarse-grained molecule. The molecules are then combined, solvated, minimized, and equilibrated with position restraints. Validation of the process was conducted on a pure POPC membrane and compared with other popular methods to construct atomistic membranes. Additional examples, including surfactant self-assembly, membrane proteins, and more complex bacterial and human plasma membrane models, are also presented. By providing these examples, parameter files, code, and an easy-to-follow recipe to add new molecules, this work will aid future multiscale modeling efforts.
摘要：
软凝聚态是具有挑战性的研究由于巨大的时间和长度尺度是必要的，以准确地表示复杂的系统和捕获其基础物理。多尺度模拟对于研究具有不同时间和/或长度尺度的过程是必要的，在生物学和其他复杂系统中比比皆是。在这里，我们介绍ezAlign，用于将粗粒度分子动力学结构转换为原子表示的开源软件，允许生物分子系统的多尺度建模。ezAlignv1.1软件包可在github.com/LLNL/ezAlign上公开下载。它的基本方法是基于原子模板分子的简单比对，其次是位置约束能量最小化，这迫使原子分子采用与粗粒分子一致的构象。然后分子结合起来，溶剂化,最小化，并与位置限制相平衡。在纯POPC膜上进行了该过程的验证，并与其他常用的构建原子膜的方法进行了比较。其他示例，包括表面活性剂自组装，膜蛋白，以及更复杂的细菌和人类质膜模型，也提出了。通过提供这些例子，参数文件,代码,和一个易于遵循的配方来添加新分子，这项工作将有助于未来的多尺度建模工作。
