The molecular dynamics (MD) technique simulates atomistic or molecular interactions and movements directly through Newton's laws. While to date MD has been mainly applied to study biological systems and chemical processes, there are certain micro and nanoscale engineering applications and technologies that require an understanding of molecular phenomena in order to determine the macroscopic system behaviour. In this paper we demonstrate the application of MD to the benchmark case of the flow of a gas inside a nanochannel connecting two reservoirs with different temperatures. A mass flow is generated between the reservoirs by the thermal gradient -this phenomenon, known as the "Thermal Creep Effect", is not captured by conventional fluid dynamics with the no-slip boundary condition, and leads to unexpected macroscopic observations. We study the effect of the temperature gradient in cases with different densities and we also report the importance of the wall boundary conditions. Detailed and accurate measurements of temperature, density and pressure that are difficult to obtain through experiments are presented. MD simulations can emulate the realistic molecular conditions and flows, and yield new insight into diffusive transport in nonequilibrium gas flows. This paper demonstrates that the engineer interested in studying and designing new nanotechnologies can deploy molecular dynamics as an effective flow simulation tool.