After many months of testing, Folding@home officially rolled out a new core based on the Gromacs MD code in May 2003. Gromacs is the fastest MD code available, and likely one of the most optimized scientific codes in the world. By using hand tuned assembly code and utilizing new hardware in many PCs and Intel-based Macs (the SSE instructions), Gromacs was considerably faster than most MD codes by a factor of about 10x, and approximately a 20x to 30x speed increase over Tinker (which was written for flexibility and functionality, but not for speed).
In 2003, Gromacs had limits to what it could do, and did not support many implicit solvent models, which played a key role in our folding simulations with Tinker. Thus, while Gromacs significantly sped certain calculations, it was not a replacement for Tinker, and so the Tinker core continued to play an important role in the science of Folding@home. For these reasons, points for Gromacs WUs were set to be consistent with points for Tinker WUs. Moreover, we switched the benchmark machine to a 2.8 GHz Pentium 4 (from a 500MHz Celeron) in order to allow us to fairly benchmark these types of WUs (as the benchmark machine needed to have hardware support for SSE).