Advanced control and operation of HVAC systems in buildings is one of the most promising energy efficient technologies. However, there is still significant energy saving potential in these systems. Energy savings can come from correcting deficiencies through building commissioning. This paper focuses on deficiencies in the controls of a variable air volume (VAV) air handling unit (AHU) system. This paper demonstrates how DeST, a building simulation tool, is used to detect faults and to optimize set points in VAV AHU system controls. Through a detailed case study, this research explores the methods and values of simulation in energy performance diagnosis. The case study described in this paper was carried out as part of a commissioning project of campus buildings.