Nanotechnologies have changed this world in various aspects including the oral medicine. It has been demonstrated that silver (Ag) nanomaterials can exhibit strong inhibition and killing effect on oral bacteria. Furthermore, the Ag nanomaterials have superb antimicrobial activity and nonacute toxic effects on human cells. Previously, the impact of Ag on oral bacteria was demonstrated by experiments. In this work, we applied molecular dynamics (MD) simulations to investigate the influence of Ag nanomaterials on oral bacteria. Firstly, by comparing change of molecular structure of staphylococcal protein A (SPA) with and without Ag, we found that Ag nanomaterials have strong effect on evolution of protein secondary structure of SPA. Secondly, it was observed that Ag has negligible effect on Solvent Accessible Surface Area (SASA) of SPA indicating that the Ag only changed its microstructure. Finally, it was found that the average amount of hydrogen bond in SPA was reduced in the presence of Ag which was origin of antimicrobial activity of Ag. It is believed that the growing interest in dental medicine with nanomaterials would lead molecular dynamics simulations to be an effective method for studying inhibition and killing pathological process of nanomaterials on oral bacteria.