I use Rosett_3.3 to design a protein whose length is 166. And the command is
fixbb.linuxgccrelease -s protein.pdb -resfile protein.resfile -ex1 -ex2 -nstruct 1 -database $ROSETTA_DATABASE -jran 111111 -fast_sc_moves True
However, it takes me more than 2 hour to finish the job. I use rosetta 2.3 to design the same protein with the same parameter. It takes me only 1-2 minutes.
Could you please tell me what parameters should I use to make the program fast?