TY  - EJOU
AU  - Han, Zhiyi  
AU  - Huang, Yugai  
AU  - Xie, Xiaoqiang  
AU  - Mei, Ying  
AU  - Gu, Bin  

TI  - The Algorithm of Chemical Species Analysis for <i>Ab Intio</i> Molecular Dynamics Simulations and Its Application
T2  - Computers, Materials \& Continua

PY  - 2019
VL  - 59
IS  - 3
SN  - 1546-2226

AB  - In <i>ab initio</i> 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.
KW  - Chemical species
KW  -  graph theory
KW  -  algorithm
KW  -  AIMD simulations

DO  - 10.32604/cmc.2019.02181