In this paper, we investigate the selection rule for desalinating seawater using functionalized graphene sheet as a semi-permissible membrane. Both the applied mathematical modeling and MD simulations will be used to determine the acceptance conditions for water molecule or sodium ion permeating into the functionalized graphene. Both the Lennard-Jones potential and Coulomb forces are considered by taking into accounts the major molecular and ionic interactions between molecules, ions and functionalized graphene sheet. The continuous approximation will then be used to coarse grain most significant molecular and ionic interactions so that the multi-body problems could be simplified into several two-body problems and the 3D motions are reduced into degenerated 1D motion. Our mathematical model and simulations show that the negatively charged graphene always accepts sodium ions and water; however the permeability of water molecules and sodium ions becomes very sensitive to the presence of positive charges on the graphene.