In the present study, molecular dynamics (MD) simulation is performed to describe the permeation phenomena in a microporous silica membrane. The molecular flows near the system boundaries are implemented through dual control volume grand canonical molecular dynamics (DCV-GCMD) method, which is a combination of molecular dynamics (MD) simulation and grand canonical Monte Carlo (GCMC) method. Helium, nitrogen and carbon dioxide gases are used as permeating materials. The permeations of pure gases and mixtures are carried out using DCV-GCMD method. To evaluate the membrane performance, the permeability for each case is predicted and compared with experimental data for various operating conditions. The parameters of activated diffusion model are estimated for each gas. For the mixtures, a comparison is made between the separation factor and the permselectivity. The separation mechanisms are identified through the analyses of the simulation results.