This code uses Molecular Dynamics (MD) strategies to simulate benzene molecules in a vacuum. It started as a final project for the Computational Methods of Physics course taught in the physics department at Arizona State University, where the original authors, Nikolaus Awtrey, Justin Gens, and Ricky Sexton, were able to view the generated trajectories using Visual Molecular Dynamics (VMD). It has since had contributions made aimed at modeling Nitrogen (N2) in a vacuum to simplify the code in an attempt to develop a fully functioning model. The overarching goal is to create a model that will allow for the tuning of force field parameters by way of heat capacity to see which, if any parameters are consistent with experimental observations (for the given substance).
The basic approach is to write functions that generate positions and velocities of all atoms in the system, where the distances between the atoms in each molecule are based on experimental data and the initial velocities are determined by thermodynamics (temperature). The idea is to then integrate via the velocity Verlet algorithm and a defined set of potentials, which will determine the forces acting on each atom at every time step. The potentials currently used in this model are the Lennard-Jones and Morse potentials, but the origin plan was to include dihedral angles and electrostatic forces. With a well-defined force field and initial positions and velocities for all atoms, the system can then be integrated to create the system trajectory.