We present the results of extensive nonequilibrium Molecular Dynamics simulations of transport of a binary gas mixture of CO2 and CH4 through a carbon nanopore, in the presence of an external chemical potential or concentration gradient. The CH4 molecules are represented as Lennard-Jones (LJ) hard spheres, while the CO2 molecules are modeled both as LJ hard spheres, as well as three-site linear structures to account for their quadrupole moments. The effect of the various factors, including the structure of the pore walls, temperature, feed composition, and the molecular models and their parameters, on the transport, adsorption, and separation of the gases is investigated in detail. While the structure of the pore walls has virtually no effect on the separation factor, the temperature of the system, the pore size, and the molecular models and their parameters strongly influence it.