Boundary-Driven type Non-Equilibrium Molecular Dynamics (BD-NEMD) simulations have been carried out to investigate effusion processes of pure propane from the inside membrane to the gas phase by using two types of silicalite membrane models: an SC surface model that has an outer surface terminated at the cross section passing through the center of straight channels, and an IS surface model that has an outer surface terminated at the cross section passing through the center of intersections. In all simulations, the silicalite membrane and the propane molecule are represented by flexible (movable) models. It is found that the average effusion flux and the local density around the outer surface for the IS surface model are larger than those for the SC surface model. The potential and kinetic energy profiles have shown that effusing molecules take extra kinetic energy from membrane atoms to go over the potential barrier at the membrane exit. It is suggested that the existence of weak adsorption sites on the outer surface is essentially important for inorganic membranes to have high permeation fluxes.