Solvent simulation implicit solvation methodology

Over the recent years implicit solvent models have undergone a transition to relatively mature methodology that is now widely employed in molecular dynamics simulations and related applications. Most popular are implicit solvent models based on a decomposition of the solvation free energy into electrostatic and nonpolar components. The electrostatic free energy is typically obtained according to a continuum electrostatics model that is described by Poisson theory or by the more approximate but much more efficient Generalized Born formalism. 

An accurate description of the aqueous environment is essential for atom-level biomolec-ular simulations, but may become very expensive computationally. An imphcit model replaces the discrete water molecules by an infinite continuum medium with some of the dielectric and hydrophobic properties of water. The continuum implicit solvent models have several advantages over the explicit water representation, especially in molecular dynamics simulations (e.g., they are often less expensive, and generally scale better on parallel machines they correspond to instantaneous solvent dielectric response the continuum model corresponds to solvation in an infinite volume of solvent, there are no artifacts of periodic boundary conditions estimating free energies of solvated structares is much more straightforward than with explicit water models). Despite the fact that the methodology represents an approximation at a fundamental level, it has in many cases been successful in calculating various macromolecular properties (Case et al. 2005). 

---