Department of Biochemistry, University of Oxford, Oxford, UK.
School of Chemistry, University of Southampton, Southampton, UK.
Methods Mol Biol. 2021;2302:253-273. doi: 10.1007/978-1-0716-1394-8_14.
Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and length scales and as a result a multiscale approach must be adopted. One such approach is coarse-graining, where biochemical accuracy is sacrificed for computational efficiency. Here, we present a practical guide to setting up and carrying out coarse-grained molecular dynamics simulations.
当前的计算机体系结构，结合最先进的分子动力学模拟软件，使得深入研究大型生物分子系统的细节成为可能。然而，生物现象发生在不同的时间和长度尺度上，因此必须采用多尺度方法。其中一种方法是粗粒化，在这种方法中，牺牲了生化精度以提高计算效率。在这里，我们提供了一个实用指南，介绍如何设置和进行粗粒化分子动力学模拟。
