隐式水模型.pdfVIP

P1: FRK August 12, 2000 12:31 Annual Reviews AR109-05 Annu. Rev. Phys. Chem. 2000. 51:129–52 Copyright c 2000 by Annual Reviews. All rights reserved GENERALIZED BORN MODELS OF MACROMOLECULAR SOLVATION EFFECTS Donald Bashford and David A. Case Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037; e-mail: bashford@, case@ Key Words solvation energy, continuum dielectrics ■ Abstract It would often be useful in computer simulations to use a simple de- scription of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermo- dynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational ef?ciency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its ?delity to the underlying continuum model and for its ability to replace explicit con- sideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore ?t most naturally into conventional molecular mechanics calculations. INTRODUCTION There are many circumstances in molecular modeling studies where a simpli?ed description of solvent effects has advantages