Abstract: PCFF and COMPASS force fields were used to describe PDMS and PS1 polymeric systems and to estimate the diffusion coefficient of N2 and O2 through the PDMS and PS1 matrices at 298 K by molecular dynamics simulation.It was found that the COMPASS force field was better in describing the transport behavior of the penetrants.The calculated densities after refinement were in good agreement with the experimental results.The group-based and Ewald summation skills were used to estimate the non-bonded interaction between atoms.Calculation using the Ewald summation method took much longer time without bringing in obvious improvement in density estimation.Various cut-offs in using the group-based summation method did not produce densities with much difference, and the cut-off of 1.3 nm was the best.Two types of diffusions of the small molecules in the polymers were discussed.The diffusion of O2 and N2 in PDMS could be transformed from anomalous to normal motion in 30 ps; while their diffusion in PS1 would take 300 ps transforming from anomalous to normal state.The trajectories of diffusion of N2 and O2 in PDMS or PS1 were different.The motion area of O2 in the PS1 was much larger than N2; however, the former in the PDMS matrix was only slightly larger than the latter.The diffusions of O2 and N2 in the PDMS and PS1 were consistent with the free volumes of polymers.