The permeation of He, CO2, and N2 through a thin silica membrane was investigated using molecular dynamics. The permeance of He follows Knudsen flow. The permeation of CO2 is higher than the estimated value from Knudsen theory. Inside the pore, CO2, tends to be parallel to the pore wall. This orientation is suitable for diffusion. In contrast, N2, shows lower permeance compared to the value from Knudsen theory. The molecules present perpendicular orientations inside the pore wall, which reduces their diffusion. In mixed CO2/N2, gas simulation, the selective permeation of CO2 relative to N2 was observed.