We present a molecular dynamics (MD) methodology to investigate temperature-driven gas flow through a nanochannel connecting two reservoirs at different temperatures. The temperature gradient along the channel drives the macroscopic movement of gas molecules from the cold to the hot regions, in the phenomenon known as thermal transpiration. Temperature, density and pressure profile variations along the axial direction are measured at various rarefaction conditions, from the slip flow to the free molecular regimes. Pressure and density evolutions are monitored as a function of time in both the hot and cold reservoirs. The normalized thermo molecular pressure difference (TMPD) values are calculated and compared with kinetic theory results. Comparisons show good agreement up to the early transition regime, although beyond this our numerical experiments over-predict the theoretical results. These numerical experiments are useful because experimental data is scarce for nano devices and these molecular simulations can mimic realistic conditions. © 2012 American Institute of Physics.