Adapting the inducible multipole solvation model for use in molecular dynamics simulations

The environment of a macromolecule has a crucial influence on its structure and function. In theoretical simulation studies the molecules comprising the environment are either explicitly included or an implicit representation is used which models their effect. One common example of the latter approach is to determine the electrostatic interactions between the solvent and the macromolecule by solving the Poisson-Boltzmann equation for the system. Recently Davis has developed a model, the inducible multipole solvation model, that aims to mimic the effect of solvation by providing an approximation to the solution of the Poisson equation. This Letter discusses the model and some modifications to it and shows how the method can be used to calculate the electrostatic interactions for a system during a molecular dynamics simulation.