The flux of methane through the straight channels of thin silicalite membranes is studied via dual control volume grand canonical molecular dynamics. The adsorption layers on the surfaces of the thin membranes are found to provide a significant resistance to the flux of methane. This strong surface effect for thin membranes requires that the control volumes (where insertions and deletions are performed) must be placed far enough away from the membrane surface that they do not overlap with the surface adsorption layer. The permeance (flux/pressure drop) of methane through the surface layer is shown to be insensitive to both the average pressure and the pressure drop. In contrast, the permeance through the interior of the membrane increases with decreasing average pressure. These results are explained using a model which treats the transport through the surface barrier as driven by the pressure gradient and transport through the zeolite as driven by the chemical potential gradient. A new force field named DACNIS is presented which accurately describes the adsorption isotherms of methane and ethane in silicalite.