The Whole Atmosphere Community Climate Model (WACCM) version 2 extends from the ground to the lower thermosphere. It is built on the NCAR/Community Atmosphere Model (CAM) version 2, but WACCM implements also physical and chemical packages for the middle and upper atmosphere. The model describes accurately the radiative budget, taking into account non-LTE processes above 70 km, and the momentum budget, which includes a source due to breaking of gravity waves. In this talk we discuss the role that the spectrum of gravity waves has on the circulation, thermal structure and composition of the middle atmosphere. We show the important role that gravity waves transport and heating have on the thermodynamic budget and structure near the mesopause.