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

Published: 14 March 2022| Version 1 | DOI: 10.17632/s7dsk553fh.1
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Description

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.

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Physical Chemistry, Computational Physics, Molecular Dynamics, Hydrocarbon

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