LAMMPS framework for dynamic bonding and an application modeling DNA

This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected tri... Title of program: LAMMPS Framework for Directional Dynamic Bonding Catalogue Id: AEME_v1_0 Nature of problem Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics. Versions of this program held in the CPC repository in Mendeley Data AEME_v1_0; LAMMPS Framework for Directional Dynamic Bonding; 10.1016/j.cpc.2012.03.005本程序源自贝尔法斯特女王大学馆藏的CPC程序库（1969-2018年）。 摘要：本研究对大型原子/分子大规模并行模拟器（Large-scale Atomic/Molecular Massively Parallel Simulator，LAMMPS）进行了功能扩展，使其支持方向性键合与动态键合过程。该框架可实现新键的随机生成、现有键的断裂以及键型间的相互转换。通过调控键合过程，可限制粗粒珠针对各类键型的最大官能度。伴随键合动态变化，新连接的三单元结构间的角相互作用与二面角相互作用亦将被动态引入（原文此处存在截断）。 程序名称：面向方向性动态键合的LAMMPS框架 目录编号：AEME_v1_0 待解决问题：模拟具备化学反应特性的粗粒化模型，例如DNA杂交动力学过程。 孟德尔莱数据（Mendeley Data）的CPC库中收录的本程序版本信息：AEME_v1_0；面向方向性动态键合的LAMMPS框架；DOI:10.1016/j.cpc.2012.03.005