Programming GPUs with CUDA
NVIDIA CUDA™ technology is a C language environment that enables programmers and developers to write software to solve complex computational problems in a fraction of the time, in suitable codes, by tapping into the many-core parallel processing power of GPUs. CUDA-capable GPUs can be used to accelerate applications—from video and audio encoding to oil and gas exploration, product design, medical imaging, and scientific research.
Please note that OpenCL is an emerging open standard that can also be used to access these cards (and hardware that isn't NVIDIA from ATI/AMD).
CUDA-ready drug discovery packages (2009) PPT with links
Notes on port of amber (v11) to nVidia GPGPUs
"CUDA, Supercomputing for the Masses" 20-part tutorial from Dr. Dobb's Journal.
The University of Manchester is also developing a CUDA module as part of its forthcoming GPU Courses.