Reaction analysis and visualization of ReaxFF molecular dynamics simulations

Area of Science:

• Computational Chemistry
• Materials Science
• Chemical Engineering

Background:

• Reactive Force Field Molecular Dynamics (ReaxFF MD) is valuable for studying complex chemical reactions in large systems.
• Current ReaxFF MD analysis tools cannot directly capture chemical reactions from simulation trajectories, hindering reaction mechanism exploration.

Purpose of the Study:

• To introduce VARxMD, a novel tool for the Visualization and Analysis of Reactive Molecular Dynamics simulations.
• To enable detailed chemical reaction analysis and visualization directly from ReaxFF MD trajectories.

Main Methods:

• VARxMD analyzes atomic connectivity, bond orders, and 3D coordinates from simulation trajectories.
• It identifies molecular fragments, chemical species (molecules or radicals), and detects bond breaking/forming events.
• Automatic generation of detailed chemical reactions between simulation frames.

Main Results:

• VARxMD successfully analyzes and visualizes chemical reactions within ReaxFF MD trajectories.
• The tool was applied to coal and high-density polyethylene (HDPE) pyrolysis simulations.
• Demonstrated capability in exploring complex reaction mechanisms in large-scale systems.

Conclusions:

• VARxMD is the first specialized tool for reaction analysis and visualization in ReaxFF MD.
• It overcomes limitations of existing tools by directly analyzing reaction pathways.
• VARxMD facilitates the study of complex chemical reactions in large molecular systems, such as pyrolysis.