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The permeation of methane molecules through the silicalite-1 surfaces with and without silanol groups has been studied by nonequilibrium molecular dynamics computer simulations. A newly fitted intermolecular potential between the methane molecules and the silanol is used. A control volume provides a nearly stationary gas phase close to the membrane. The nonequilibrium process of filling the (initially empty) membrane with methane molecules until saturation is considered, and the surface permeability has been evaluated. It turns out to be strongly influenced by the presence of silanol groups. Additionally it was found that for a large part of the loading process the particle stream into the zeolite membrane was nearly independent upon the deviation from equilibrium. This means that far from equilibrium the decay of this deviation does not follow an exponential law.