The accuracy of the peptide simulations supports the use of our non-bonded and modified Seminario bonded parametrization strategies. In protein MD simulations, the RMSD of the backbone atoms relative to experimental structures remained low, below 2 Å, for two of the five proteins tested. The α-helices present in all of the proteins generally remained close to the experimental structures, but the β-sheets exhibited greater loss of structure, and regions with no clear structure or exhibiting a turn regularly deviated from the starting structure.