Comparison of a GB solvation model with explicit solvent simulations:  Potentials of mean force and conformational preferences of alanine dipeptide and 1,2-dichloroethane

The potential of mean force in aqueous solution for rotation around the two backbone dihedrals φ and ψ of the alanine dipeptide is computed in explicit water and in the continuum approximation by numerical integration of the self-energies and the generalized Born (GB) equation. The two models show good agreement. The experimentally observed increase in the gauche/trans population ratio for dichloroethane in going from the gas phase to the pure liquid is reproduced by the GB solvation model with a solvent dielectric constant of 10.5. This test case shows that the GB model gives accurate predictions also for solvents with much lower polarizability than water. For both test systems additional calculations with a finite difference Poisson equation solver yield somewhat more accurate results at a much higher computational cost than the GB solvation model.