This research studies Graphene Quantum Dots (GQDs) adsorption on Staphylococcus aureus surface protein G (SasG) using the molecular dynamics simulation method that in addition to investigating various aspects of adsorption, including edge and surface effects of GQDs, and effects of orientation and size of GQDs, proposes a new study method in edge effects studies. Through our simulations to find edge effects, we found that even if GQD approaches the protein with its edges, GQDs’ edges are not freely adsorbed on the protein because when the particles interact with each other, GQD rotates and then adsorbs the protein with its surface; therefore, GQD having initial velocity was applied to the protein to force the protein to interact with GQDs’ edges to find both surface and edge effects. This is a new way of investigating that we propose to study edge effects in the molecular dynamics simulation method.