There are lots of differences between GPUs and this leads to big swings in PPD when proteins of different sizes are simulated. When we benchmark on a given machine, we can ensure that on a machine that is similar to the benchmark machine, there will be no fluctuation in PPD. For machines which are very different from the benchmark machine, there could be big swings (33% is not unheard of, considering the large differences in hardware, such as the number of shaders, from GPU to GPU). This is particularly true for NVIDIA cards, which do very well at small proteins compared to the benchmark machine, but not nearly as well for larger proteins.
