Perylene molecules could be used to make inexpensive solar panels if these flat molecules can be arranged into ordered structures. In this work we investigate how the distribution of electrical charges on perylene molecules influence how they self-assemble using molecular dynamics simulations. Using the HOOMD-blue simulation package and leveraging Boise State’s supercomputer cluster “Kestrel”, we perform hundreds of simulations of perylene to evaluate how the structure of 10, 100, and 1000-molecule aggregates change with temperature and partial charge. We observe the differences in self-assembly of perylene using the 3-D molecular visualization program VMD and we quantify simulation equilibration using the potential energy. The equilibrated morphologies from our simulations are compared against perylene arrangements from scattering experiments. We find that a positively charged rim and negatively charged center make the molecules less likely to form columnar stacks, which explains the differences between experimental perylene measurements and simulations of uncharged molecules.