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

Zhiyi Han1, Yugai Huang2,3, Xiaoqiang Xie1, Ying Mei1, Bin Gu1,*

Jiangsu Key Laboratory for Optoelectronic Detection of Atmosphere and Ocean, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
Department of Chemistry, Jiangsu Second Normal University, Nanjing, 210013, China.
Queen’s University, Belfast, Northern Ireland, Belfast BT7 1NN, United Kingdom.

* Corresponding Author: Bin Gu. Email: .

Computers, Materials & Continua 2019, 59(3), 995-1003.


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.


Cite This Article

Z. Han, Y. Huang, X. Xie, Y. Mei and B. Gu, "The algorithm of chemical species analysis for ab intio molecular dynamics simulations and its application," Computers, Materials & Continua, vol. 59, no.3, pp. 995–1003, 2019.

This work is licensed under a Creative Commons Attribution 4.0 International License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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