Bogetti Anthony T, Mostofian Barmak, Dickson Alex, Pratt A J, Saglam Ali S, Harrison Page O, Adelman Joshua L, Dudek Max, Torrillo Paul A, DeGrave Alex J, Adhikari Upendra, Zwier Matthew C, Zuckerman Daniel M, Chong Lillian T
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA.
Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR.
Living J Comput Mol Sci. 2019;1(2). doi: 10.33011/livecoms.1.2.10607. Epub 2019 Oct 4.
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we present five tutorials instructing users in the best practices for preparing, carrying out, and analyzing WE simulations for various applications using the WESTPA software. Users are expected to already have significant experience with running standard molecular dynamics simulations using the underlying dynamics engine of interest (e.g. Amber, Gromacs, OpenMM). The tutorials range from a molecular association process in explicit solvent to more complex processes such as host-guest association, peptide conformational sampling, and protein folding.
加权系综（WE）策略已被证明在使用原子分子动力学模拟为蛋白质折叠和蛋白质结合等罕见事件生成路径和速率常数方面非常高效。在这里，我们提供五个教程，指导用户使用WESTPA软件为各种应用准备、进行和分析WE模拟的最佳实践。预计用户已经在使用感兴趣的基础动力学引擎（如Amber、Gromacs、OpenMM）运行标准分子动力学模拟方面有丰富经验。这些教程涵盖了从明确溶剂中的分子缔合过程到更复杂的过程，如主客体缔合、肽构象采样和蛋白质折叠。
