Explicit and GB/SA solvents: Each with two different force fields in multicanonical conformational sampling of a 25-residue polypeptide

We compared effects of implicit (GB/SA) and explicit (TIP3P) solvents on physical quantities of a 25-residue polypeptide by performing multicanonical molecular dynamics simulations. To assess the effects systematically, we examined two intra-polypeptide force fields for each solvent model. The force fields have different secondary-structure propensities. We computed the temperature dependence of helix content, radius of gyration, end-to-end distance, and free-energy landscape. These physical quantities showed large differences between the two solvent models in each force field. For instance, the most thermodynamically stable conformation from the GB/SA solvent was an α-helix, although that from the TIP3P solvent was a β-sheet.