Generalized born models of macromolecular solvation effects

It would often be useful in computer simulations to use a simple descriptio n of solvation effects, instead of explicitly representing the individual s olvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive be cause of their computational efficiency. Here we give an overview of one su ch approximation, the generalized Born model, which is simple and fast enou gh to be used for molecular dynamics simulations of proteins and nucleic ac ids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consider ation of solvent molecules in macromolecular simulations. We focus particul arly on versions of the generalized Born model that have a pair-wise analyt ical form, and therefore fit most naturally into conventional molecular mec hanics calculations.