Jiang Fan, Geng Hao
Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.
Methods Mol Biol. 2019;2001:61-71. doi: 10.1007/978-1-4939-9504-2_4.
Molecular dynamics (MD) simulations play more and more important roles in studying conformations of cyclic peptides in solution. Here we describe how to use replica-exchange molecular dynamics (REMD) implemented in Gromacs software package to simulate peptides with backbone cyclization and stapled peptides with side-chain linkages. Some of our methods for trajectory analyses and our residue-specific force fields are also described.
分子动力学（MD）模拟在研究溶液中环肽的构象方面发挥着越来越重要的作用。在此，我们描述了如何使用Gromacs软件包中实现的副本交换分子动力学（REMD）来模拟具有主链环化的肽和具有侧链连接的订书肽。我们还描述了一些轨迹分析方法和残基特异性力场。
