I've just learned that there's a new version of the AMBER molecular dynamics program available, capable of using GPUs.

http://ambermd.org/
http://www.simbiome.org/resource/show/72
http://msc.psu.edu/tutorials/IntroAmber_course.pdf
http://www.nvidia.com/object/molecular_dynamics.html
http://www.rosswalker.co.uk/tutorials/amber_workshop/
http://www.wmd-lab.org/

You may want to look at its web pages and decide if it's suitable for what's done at GPUGRID.