A new grid-based algorithm developed at Molecular Simulations, and molecular dynamics method have been applied to modeling the locations of non-framework species in zeolites. This new method locates the energy minima for various frameworks and populates these sites with the non-framework species. The cation locations were predicted in dehydrated zeolite adsorbents and catalysts, such as Na88X, Ca48X, mixed cation zeolite 3A (K(60)Na(36)A), and Cu-mordenite (Si/Al=5.0) using only well-known framework structure models. Furthermore, the locations of benzene molecules in a supercage of zeolite Ca48X were correctly predicted via the application of the Monte Carlo docking and molecular dynamics methods. These examples demonstrate that when the framework type is known, the new technique can provide a realistic initial structure input for the challenging task of solving crystal structures of zeolites containing non-framework species.