Zhiyi Han1, Yugai Huang2,3, Xiaoqiang Xie1, Ying Mei1, Bin Gu1,*
CMC-Computers, Materials & Continua, Vol.59, No.3, pp. 995-1003, 2019, DOI:10.32604/cmc.2019.02181
Abstract 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. More >
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