An implementation of the MM3 molecular dynamics code written in MATLAB This code makes it possible to let an atomic system evolve in time. GenerateAtoms.m is used to generate the positions of a benzene ring. MolecularDynamics.m is a driver file to run a simulation on benzene. Energy.png shows the potential energy as the simulation is run and Vibrations.png shows how the bond lengths change in time. sim.avi shows the molecule moving in time. Report.pdf shows a summary of how I implemented the MM3 forcefield along with challenges encountered along the way.
Matlab 2019 or later