Guys, I'm working with ab initio, homology modeling and docking. I realized running abinitio and modeling by homology the MPI automatically chooses how it will be run the job. The problem is that the abinitio is running easy, but the homology modeling running on the server is so slow as running on my pc simple laboratory by analyzing the output files realized that the homology modeling is used this Procolo (protocols.jd2. MPIFileBufJobDistributor), and abinitio (protocols.jobdist.JobDistributors) which is efficient in my view.
My question is, how to choose the best protocol, for example, reading material rosetta from what I understand the best protocol for homology modeling would be jd 2 :: mpi_work_partition_job_distributor, and the abinitio would be MPIFileBufJobDistributor.
Someone help me?