High quality GaN films on AlN buffer layers were grown on Si(111) with a new, commercial, two-injector vertical rotating disk MOCVD reactor (CVD, Inc.). It was found that the geometry of the susceptor greatly affected the structural quality of the epilayers on Si. For the original susceptor geometry, though single crystal GaN films could be obtained, the films were dark gray in appearance with a rough morphology, and the best x-ray rocking curve FWHM was 2.33°. After modifying the susceptor geometry, transparent, mirror-like single crystal GaN films were obtained with the best x-ray rocking curve FWHM being 0.24°. Photoluminescence (PL) and infrared reflectance (IR) spectra of the grown films were compared. The film growth rate was found to increase with decrease of the growth pressure. A 2-D simulation of the flow, heat transfer, and chemical species transport in the reactor showed a more symmetric flow, larger velocity gradient, and lower upward velocity with the modified susceptor, which may be the main reason for the improvement of the structural quality of the films.