Modeling chemical reactions in classical molecular dynamics simulations
Modeling chemical reactions in classical molecular dynamics simulations
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DOI：
10.1016/j.polymer.2017.09.038
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发表时间：
2017-10-16
期刊：
影响因子：
4.6
通讯作者：
Wise, Kristopher E.
中科院分区：
文献类型：
--
作者：
Gissinger, Jacob R.;Jensen, Benjamin D.;Wise, Kristopher E.
在LAMMPS （Large-scale Atomic molecular Massively Parallel Simulator）的框架下，提出了一种将多步反应机制整合到传统固定价力场原子分子动力学模拟中的算法。这个扩展，称为固定键/反应，使键的拓扑修改期间运行的MD模拟使用前和反应后的键合模板，以执行预先指定的反应。候选反应物首先通过原子间分离确定，然后应用广义拓扑匹配算法来确认它们与反应前模板匹配。随后是匹配反应后模板的拓扑转换和最小化高能构型的动态弛豫。模拟了尼龙6,6的缩聚和高交联环氧树脂的形成两个案例，以证明该算法的鲁棒性、稳定性和速度。讨论了可以提高其效用的改进。Elsevier Ltd.出版。
An algorithm capable of incorporating multi-step reaction mechanisms into atomistic molecular dynamics simulations using traditional fixed valence force fields is proposed and implemented within the framework of LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator). This extension, referred to as fix bond/react, enables bonding topology modifications during a running MD simulation using pre- and post-reaction bonding templates to carry out a pre-specified reaction. Candidate reactants are first identified by interatomic separation, followed by the application of a generalized topology matching algorithm to confirm they match the pre-reaction template. This is followed by a topology conversion to match the post-reaction template and a dynamic relaxation to minimize high energy configurations. Two case studies, the condensation polymerization of nylon 6,6 and the formation of a highly-crosslinked epoxy, are simulated to demonstrate the robustness, stability, and speed of the algorithm. Improvements which could increase its utility are discussed. Published by Elsevier Ltd.