That GROMACS looks very nice (thanks Luca!) and I'll give it a try. Althought I'm not pretty sure whether this performs the same actions as http://www.stanford.edu/group/pandegroup/folding/ -- BTW, that's what I meant with "protein folding".
Folding@home uses the Gromacs core. Snip from log file: [04:03:05] + Processing work unit [04:03:05] Core required: FahCore_78.exe [04:03:05] Core found. [04:03:05] Working on Unit 09 [May 5 04:03:05] [04:03:05] + Working ... [04:03:05] [04:03:05] *------------------------------* [04:03:05] Folding@home Gromacs Core [04:03:05] Version 1.62 (April 2, 2004) [04:03:05] [04:03:05] Preparing to commence simulation [04:03:05] - Assembly optimizations manually forced on. [04:03:05] - Not checking prior termination. [04:03:05] - Expanded 197783 -> 955477 (decompressed 483.0 percent) [04:03:05] - Starting from initial work packet [04:03:05] [04:03:05] Project: 1042 (Run 5, Clone 66, Gen 2) [04:03:05] [04:03:05] Assembly optimizations on if available. [04:03:05] Entering M.D. [04:03:11] Protein: p1042_nat96_273 [04:03:11] [04:03:11] Writing local files [04:03:11] Extra SSE boost OK. [04:03:11] Writing local files [04:03:11] Completed 0 out of 2500000 steps (0%) [04:13:26] Writing local files [04:13:26] Completed 25000 out of 2500000 steps (1%)