Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
J Chem Phys. 2020 Aug 7;153(5):054123. doi: 10.1063/5.0013849.
Before beginning the production phase of molecular dynamics simulations, i.e., the phase that produces the data to be analyzed, it is often necessary to first perform a series of one or more preparatory minimizations and/or molecular dynamics simulations in order to ensure that subsequent production simulations are stable. This is particularly important for simulations with explicit solvent molecules. Despite the preparatory minimizations and simulations being ubiquitous and essential for stable production simulations, there are currently no general recommended procedures to perform them and very few criteria to decide whether the system is capable of producing a stable simulation trajectory. Here, we propose a simple and well-defined ten step simulation preparation protocol for explicitly solvated biomolecules, which can be applied to a wide variety of system types, as well as a simple test based on the system density for determining whether the simulation is stabilized.
在开始分子动力学模拟的生产阶段（即产生要分析的数据的阶段）之前，通常需要首先进行一系列一个或多个预备的最小化和/或分子动力学模拟，以确保后续的生产模拟是稳定的。这对于具有显式溶剂分子的模拟尤为重要。尽管预备的最小化和模拟是稳定生产模拟所必需的，但目前还没有通用的推荐程序来执行这些模拟，也几乎没有标准来决定系统是否能够产生稳定的模拟轨迹。在这里，我们提出了一个简单而明确的十步模拟准备方案，用于显式溶剂化的生物分子，该方案可应用于各种系统类型，以及一个基于系统密度的简单测试，以确定模拟是否稳定。
