Molecular mechanics and dynamics of biomolecules using a solvent continuummodel

An easy implementation of molecular mechanics and molecular dynamics simula tion using a continuum solvent model is presented that is particularly suit able for biomolecular simulations. The computation of solvation forces is m ade using the linear Poisson-Boltzmann equation (polar contribution) and th e solvent-accessible surface area approach (nonpolar contribution). The fea sibility of the methodology is demonstrated on a small protein and a small DNA hairpin. Although the parameters employed in this model must be refined to gain reliability, the performance of the method, with a standard choice of parameters, is comparable with results obtained by explicit water simul ations. (C) 2001 John Wiley & Sons, Inc.