The executeable released with 3.1 is not MPI compatible. I can get you an MPI compatible version if you need one.
MPI does not speed up Rosetta. When Rosetta runs in MPI, it runs independent trajectories on each processor. So, 500 independent Rosetta instances will create 500 structures in the same amount of time as one 500-way MPI instance on 500 processors. The advantage to MPI is A) non-independent processors can communicate, meaning that they can output to a shared directory without overwriting each others’ results (rather than running in 500 directories), and some clusters won’t LET you run without MPI.