Protein aggregation is associated with serious and eventually-fatal neurodegenerative diseases including Alzheimer’s , Parkinson’s and the prion diseases. While atomic resolution molecular dynamics simulations have been useful in this regard, they are limited to examination of either oligomer formation by a small number of peptides or analysis of the stability of a moderate number of peptides placed in trial or known experimental structures. We describe large scale molecular dynamics simulations of the spontaneous formation of fibrils by systems containing large numbers of peptides. The simulations are fast enough to enable us to follow the steps in the aggregation process from an initial configuration of random coils to oligomers and then to proto-filaments with cross-β structures. In simulations of Aβ17-42 peptides we uncovered two fibrillization mechanisms that govern their structural conversion from disordered oligomers into protofilaments. We also investigate the influence of crowding agents on oligomerization and fibrillization for Aβ16-22. Simulations are conducted which allow examination of the impact of naturally-derived inhibitors (resveratrol, curcumin, vanillin, and curcumin) on the oligomerization and fibrillation of A β17-36. Finally we describe simulations of human, mouse and Syrian Hamster fragments of the prion protein, PrP(120-144), in effort to understand cross seeding. The results of all of the simulations are compared to experiment. Movies of the aggregation process on a molecular level will be shown.