I am doing homology modeling on a ~200 amino acid protein. According to the online manual, I plan to generate 10000 decoys. However, it would take very long time (about 20 days) to finish the job using a single processor on my machine. So I tried the " -run:constant_seed -run:jran " options which is suggested in Abinitio protocol. Then I submitted multiple jobs with different "jran" seeds.
Does this work? If not, please give some suggestions!
Thanks a lot!