The School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
RADICAL, ECE, Rutgers University, Piscataway, NJ, USA.
Methods Mol Biol. 2021;2302:335-356. doi: 10.1007/978-1-0716-1394-8_18.
Molecular dynamics or MD simulation is gradually maturing into a tool for constructing in vivo models of living cells in atomistic details. The feasibility of such models is bolstered by integrating the simulations with data from microscopic, tomographic and spectroscopic experiments on exascale supercomputers, facilitated by the use of deep learning technologies. Over time, MD simulation has evolved from tens of thousands of atoms to over 100 million atoms comprising an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium. In this chapter, we present a step-by-step outline for preparing, executing and analyzing such large-scale MD simulations of biological systems that are essential to life processes. All scripts are provided via GitHub.
分子动力学（MD）模拟正逐渐成为构建活细胞体内模型的工具，可以详细呈现原子结构。通过在超级计算机上结合微观、断层扫描和光谱实验数据进行模拟，并利用深度学习技术，此类模型的可行性得到了增强。随着时间的推移，MD 模拟已经从数万个原子扩展到 1 亿多个原子，涵盖了整个细胞细胞器，甚至是来自紫色细菌的光合色素囊泡。在本章中，我们提供了一个逐步的概述，用于准备、执行和分析对生命过程至关重要的此类大规模生物系统的 MD 模拟。所有脚本都可以通过 GitHub 获取。
