Non-equilibrium molecular dynamics simulations of pure carbon dioxide and methane and their equimolar mixtures have been carried out with an external driving force imposed on carbon slit pores to investigate gas slippage and Klinkenberg effects. Simulations were conducted to determine the effect of pore size and exposure to an external potential on the velocity profile and slip-stick boundary conditions. The simulations indicate that molecule-wall collisions influence the velocity profile, which deviates significantly from the Navier-Stokes hydrodynamic prediction for micro- and mesopores. Also, the shape of the velocity profile is found to be independent of the applied pressure gradient in micropores. The results indicate that the velocity profile is uniform for pore sizes less than 2 nm (micropores) where the transport is mainly due to molecular streaming or Knudsen diffusion and, to a lesser extent, molecular diffusion. As pore sizes increase to 10 nm, parabolic profiles are observed due to the reduced interaction of gas molecules with the pore walls. A 3D pore network, representative of porous carbon-based materials, has been generated atomistically using the Voronoi tessellation method. Simulations have been carried out to determine the effect of the pore structure and modeled viscosity on permeability and Klinkenberg parameters. The use of the bulk-phase viscosity for estimating the permeability of CO(2) in units of Darcy in a 3D micropore network is not an appropriate assumption as it significantly underestimates the CO(2) permeability. On the other hand, since the transport properties of CH(4) are less influenced by the pore walls compared with CO(2), the use of the bulk-phase CH(4) viscosity estimates are a reasonable assumption.