Calculation of Molecular Dynamics for Peptides in Dimethyl Sulfoxide: Elimination of Vacuum Effects

The γ turns not found experimentally in cyclic hexapeptides are also not found in molecular dynamics (MD) simulations if the calculations take the surrounding solvent into consideration. In this report the structures obtained from simulations conducted for the peptide in vacuum were used in subsequent simulations with dimethyl sulfoxide as the solvent. The two γ turns originally obtained disappeared, and only the experimentally proven β turns remained. These results show that the solvent must be explicitly included in MD simulations of peptide conformations in solutions.