Moller-Plesset perturbation-based potentials have been used in molecular dynamics simulations to examine methane diffusion in silicalite-1. The simulation box contains 2 unit cells of silicalite-1 and varying loading numbers (n(ld)) from 1, 2, 3, to 4 methane molecules per intersection, corresponding to 8, 16, 24, and 32 molecules per simulation box, respectively. Consistent with the previous study, a preferential diffusing path for methane is close to the channel axes. The structure of the methane molecules in the silicalite-1 pore was exhibited in terms of the methane-methane radial distribution function (RDF) in which the first peak appears at 6.4 angstrom for n(ld) <= 2, becomes a broad maximum at n(ld) = 3, and splits into two sharp peaks centered at 6.4 and 8.6 angstrom at n(ld) = 4. This fact can be clearly described by an intensification of the methane density in the straight and zigzag channels but a decrease in the intersection when the loading increases. These features of the observed RDFs are in contrast with the previous report using a molecular dynamics force-field potential in which the RDFs for all concentrations show first maxima at similar to 4 angstrom. The analysis of the relative residence times of methane at different sites inside the silicalite suggests that the zigzag channel is the most favored location. The computed self-diffusion coefficients as well as the heat of adsorptions are in reasonable agreement with the available values.