Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide

Abstract

We compute the potential of mean force (PMF) around the φ and ψ torsions of alanine dipeptide with a Poisson−Boltzmann (PB) method and compare these results to simulations in explicit water. The PB method, which includes an apolar solvation term, qualitatively reproduces the PMF profiles generated in the explicit solvent simulation at a markedly lower computational cost. These results motivate more extensive testing of continuum methods for the study of conformational and binding equilibria in solution.