The highly parallel molecular dynamics code NAMD was chosen in 2006 as a target application for the NSF petascale supercomputer now know as Blue Waters. NAMD was also one of the first codes to run on a GPU cluster when G80 and CUDA were introduced in 2007. How do the GPU-accelerated Cray XK6 Blue Waters and ORNL Titan machines compare to CPU-based platforms for a hundred-million-atom Blue Waters acceptance test? Come learn the opportunities and pitfalls of taking GPU computing to the petascale and the importance of CUDA 5 and Kepler features in combining multicore host processors and GPUs in a legacy message-driven application.