Liu Jianchuan, Lin Haiyan, Li Xun
School of Electrical Engineering and Electronic Information, Xihua University, Chengdu, 610039, China.
Institute of Linguistics, Shanghai International Studies University, Shanghai, 200000, China.
J Mol Model. 2024 Sep 3;30(9):320. doi: 10.1007/s00894-024-06119-4.
This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used in this method are described in the main text, and example input scripts are provided for the GMXPolymer code, which is based on the GROMACS molecular dynamics package. To demonstrate the efficacy of our method, we apply it to different glassy polymers exhibiting varying degrees of functionality, polarity, and rigidity. The reliability of the method is validated by comparing simulation results with experimental data in various structural and thermal properties, both of which show excellent agreement.
This work implements the GMXPolymer simulated polymerization algorithm on the GROMACS program. GMXPolymer code controls the main polymerization loop. The energy minimizations and molecular dynamics simulations use the GROMACS program called by the GMXPolymer code. A new ITP file is generated when a new bond is formed, and the necessary additions to the ITP file are made to include new bonds, angles, and dihedrals. In preparing the ITP file of the monomer, the charge of the reactive atom must be modified before the code runs so that it is a correct value after bonding.
本工作介绍了一种使用模拟聚合和分子动力学平衡来生成无定形聚合物广义结构的方法，特别关注无定形聚合物。该方法中使用的技术和算法在正文中进行了描述，并为基于GROMACS分子动力学软件包的GMXPolymer代码提供了示例输入脚本。为了证明我们方法的有效性，我们将其应用于具有不同功能度、极性和刚性的不同玻璃态聚合物。通过将模拟结果与各种结构和热性能的实验数据进行比较，验证了该方法的可靠性，两者显示出极好的一致性。
本工作在GROMACS程序上实现了GMXPolymer模拟聚合算法。GMXPolymer代码控制主要的聚合循环。能量最小化和分子动力学模拟使用由GMXPolymer代码调用的GROMACS程序。形成新键时会生成一个新的ITP文件，并对ITP文件进行必要的添加以包含新键、键角和二面角。在准备单体的ITP文件时，必须在代码运行前修改反应性原子的电荷，以便在键合后其值正确。
