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

Molecular dynamics simulations of reactive neutral chemistry in an argon‐methane plasma

“…The post‐processing utility MAFIA‐MD [ 69 ] is used to characterize the spatial structures of the formed $${{\rm{C}}}_{n}\,(n\ge 3)$$ hydrocarbons. It identifies existing structures and generates statistics of alicyclic and aromatic hydrocarbons based on the number of carbon atoms at 40 ns elapsed time.…”

“…It should be noted that the MAFIA‐MD utility does not strictly verify the four classical conditions of aromaticity according to Huckel's rule, [ 70 ] because it is impossible to extract the exact electronic structure from the trajectory files, so the conditions of $$(4n+2)\pi $$ electrons and perpendicularity of p‐orbitals cannot be checked. [ 69 ] Moreover, in molecular dynamics, the atoms of an aromatic ring are often not in the same plane at a given time. Therefore, the utility focuses only on the bond distances and the closed nature of the ring structures.…”

“…Therefore, the utility focuses only on the bond distances and the closed nature of the ring structures. [ 69 ] The idea is to extract chemical and structural information and to identify the presence of 5‐, 6‐, and 7‐membered alicyclic and aromatic ring structures in an atomic cluster. The identification of the ring structures is important because the stability of these structures, especially the aromatic rings, is considered a key to the formation and growth of dust or soot particles, as identified during combustion processes.…”

“…The post-processing utility MAFIA-MD [69] is used to characterize the spatial structures of the formed…”

A review on application of molecular simulation technology in food molecules interaction

“…In the last decade, with the progression of computer science and technology, computing power has improved by leaps and bounds, and MD simulation has begun to demonstrate its powerful ability in many fields. Particularly in the field of biological macromolecules, MD simulation increasingly showed its advantages of fast speed and high agreement with experimental results ( Baildya et al, 2022 ; Mukut et al, 2022 ; Anwar et al, 2020 ; Chamani et al, 2022 ). Mr. Martin Karplus, one of the pioneers of MD simulation, also won the Nobel Prize in chemistry in 2013.…”