How can Gromacs be that much faster?
Gromacs is built for speed. Everything about it has been optimized to be the very fastest MD code on the planet. For example, it uses the SSE instructions on Pentiums to get a 3x speed increase. 3D-Now! is supported on AMD chips. Altivec is supported on Macs. The inner loops are hand coded in assembly. It has algorithms creatively designed for speed. It’s an amazing feat. For us to include all of these optimizations into our current scientific code did not seem a judicious use of our programming resources (why reinvent the wheel?) and we instead decided to collaborate with the Gromacs team.
