Molecular arrangement and fringe identification and analysis from molecular dynamics (MAFIA-MD): A tool for analyzing the molecular structures formed during reactive molecular dynamics simulation of hydrocarbons

Reactive molecular dynamics (RMD) simulations are becoming popular, with the recent developments in high-performance and efficient computing architecture, for investigating fundamental physico-chemical behaviors of reacting species. Due to the complexity of hydrocarbon systems, characterization of molecules formed during RMD simulations of hydrocarbons can be very challenging for simulations involving a large number of molecules. The novel post-processing utility “MAFIA-MD” – an acronym for “Molecular Arrangement and Fringe Identification and Analysis from Molecular Dynamics” – presented in this manuscript can analyze and perform molecular characterization of a large number of RMD trajectory files (.XYZ files) simultaneously. The utility will be useful for analysis and chemical characterization of trajectories without the large bond information files. A graphical user interface (GUI) is developed for easy operation. The utility analyzes the existing cyclic structures in the domain and generates statistics of alicyclic and aromatic hydrocarbons based on the number of carbon atoms. Alongside the statistical analysis, the program also separates the constituent molecules and extracts their chemical information in terms of Simplified Molecular-Input Line-Entry System (SMILES) and Spatial Data File (.SDF)”. A methodology for calculating fringe spacing is also implemented in the code for validation of RMD simulation with High-Resolution Transmission Electron Microscopy (HRTEM) images.得益于高性能与高效计算架构的最新进展，反应分子动力学（Reactive Molecular Dynamics, RMD）模拟正逐渐成为研究反应物种基础物理化学行为的常用手段。由于烃类体系的复杂性，在针对含大量分子的烃类体系开展RMD模拟时，对模拟过程中生成的分子进行表征往往极具挑战。本文提出的新型后处理工具"MAFIA-MD"，其为首字母缩略词，全称为"Molecular Arrangement and Fringe Identification and Analysis from Molecular Dynamics"，即分子动力学下的分子排列与条纹识别分析，可同时对海量RMD轨迹文件（.XYZ格式文件）开展分析与分子表征工作；该工具可在无需大型键信息文件的前提下，完成轨迹的分析与化学表征。研究团队为该工具开发了配套的图形用户界面（Graphical User Interface, GUI）以简化操作。该工具可分析体系内已有的环状结构，并基于碳原子数目对脂环烃与芳香烃进行统计分析。除统计分析外，该程序还可分离体系中的组成分子，并以简化分子输入线式符号（Simplified Molecular-Input Line-Entry System, SMILES）与空间数据文件（.SDF格式）的形式提取其化学信息。代码中还集成了条纹间距计算方法，可用于结合高分辨透射电子显微镜（High-Resolution Transmission Electron Microscopy, HRTEM）图像对RMD模拟结果进行验证。