Three different molecular dynamics methods (EMD, EF-NEMD, and DCV-GCMD) were compared for the calculation of nonequilibrium transport coefficients in microporous materials. Two different pore systems were examined: An idealized pore of varying pore diameter formed from an fcc lattice of oxygen atoms, and an actual AlPO4-5 zeolite pore. For all cases, the transport coefficients calculated from EMD and EF-NEMD agreed with each other. The transport coefficient computed in a DCV-GCMD simulation varied. The results lead to the conclusion that EMD or EF-NEMD are the best methods to use when examining diffusion along a pore, and that boundary-driven techniques such as DCV-GCMD are better suited for examining interfacial transport.