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!
So long as the jobs are writing to different result files (the easiest way is to run them in separate directories) then you should get groups of different trajectories (because of different jran seeds) which can be re-combined before further analysis.