The Algorithm of Chemical Species Analysis for Ab Intio Molecular Dynamics Simulations and Its Application

• 作者: Bin Gu Xiaoqiang Xie Ying Mei Yugai Huang Zhiyi Han
• 来源期刊: 计算机、材料和连续体(英文)
• 学科: 经济
• 关键词: CHEMICAL SPECIES GRAPH THEORY ALGORITHM AIMD simulations
• 年，卷（期）: 2019,（6）
• 页码范围: 995-1003
• 页数: 9页
• 分类号: F42

摘要

In ab initio molecular dynamics(AIMD)simulations of chemical reactions,it is important but difficult to identify the chemical species in the trajectory automatically and quickly.In this paper,based on the chemical graph theory,an algorithm for molecular species identification,according to the molecular coordinates and empirical bond length database,is presented.As an example,the chemical species in condensed glycine at room temperature are investigated with our algorithm in detail.The chemical species,including canonical and zwitterionic glycine,their protonated and de-protonated states,and the free protons,are all identified,counted and recorded correctly.Potential applications and further development of the algorithm are also discussed.