RMSD calculations of each of these conformations with and without explicit harmonic hydrogen bonds were done. The primary purpose of the RMSD calculations were to see if explicitly adding harmonic hydrogen bonds would be beneficial to the model. As shown in Figure , adding explicit harmonic hydrogen bonds did not reduce the RMSD to an expected value of 0.2 nm, based on the FF. It appears that the ST conformation without the explicit harmonic hydrogen bonds has the lowest RMSD, and is even comparable to the