We developed a novel simulation technique, named as dual ensemble (DE) molecular simulation technique based on the grand canonical Monte Carlo (GCMC) method in order to treat a non-equilibrium system at which a chemical potential gradient exists, for example, membrane separation process. This technique has also integrated into two programs, dual ensemble Monte Carlo (DEMC) and dual ensemble molecular dynamics (DEMD) programs. The DEMC method treats the movement of molecules in a stochastic manner and therefore it can calculate the distribution of the molecules on the membrane surface or on the membrane pores. The DEMD program rectifies the movement of the molecules using molecular dynamics technique and therefore the permeability can be calculated directly from the simulation results. In this paper, we mainly describe the application of the DEMD program to the simulation of the CO2/N-2 gas separation with NaY membrane.