Department of Biochemistry, Virginia Tech, 111 Engel Hall, 340 West Campus Dr., Blacksburg Virginia 24061, United States.
Center for Drug Discovery, Virginia Tech, 111 Engel Hall, 340 West Campus Dr., Blacksburg Virginia 24061, United States.
J Phys Chem B. 2024 Oct 3;128(39):9418-9435. doi: 10.1021/acs.jpcb.4c04901. Epub 2024 Sep 21.
Atomistic molecular dynamics (MD) simulations have become an indispensable tool for investigating the structure, dynamics, and energetics of biomolecules. Continual optimization of software algorithms and hardware has enabled investigators to access biologically relevant time scales in feasible amounts of computing time. Given the widespread use and utility of MD simulations, there is considerable interest in learning essential skills in performing them. Here, we present a set of introductory tutorials for performing MD simulations of proteins in the popular, open-source GROMACS package. Three exercises are detailed, including simulating a single protein, setting up a protein complex, and performing umbrella sampling simulations to model the unfolding of a short polypeptide. Essential features and input settings are illustrated throughout. The purpose of these tutorials is to provide new users with a general understanding of foundational workflows, from which they can design their own simulations.
原子分子动力学（MD）模拟已成为研究生物分子结构、动力学和能量学的不可或缺的工具。软件算法和硬件的不断优化使研究人员能够在可行的计算时间内访问具有生物学相关性的时间尺度。鉴于 MD 模拟的广泛使用和实用性，人们对学习执行 MD 模拟的基本技能非常感兴趣。在这里，我们为在流行的开源 GROMACS 软件包中进行蛋白质的 MD 模拟提供了一组入门教程。详细介绍了三个练习，包括模拟单个蛋白质、设置蛋白质复合物以及进行伞状采样模拟以模拟短多肽的展开。整个过程都说明了基本功能和输入设置。这些教程的目的是为新用户提供对基础工作流程的一般理解，使他们能够设计自己的模拟。
