ddg_monomer doesn't seem to work well with mpi. I would like it to send it a job with a large amount of mutation combinations and use the mpi enabled version to finish the job quickly.
Consider the following protocol:
mpirun -np 4 /rosetta3.3/rosetta_source/bin/ddg_monomer.mpi.linuxgccrelease @ddg.flag -in:file:s min_cst_0.5.input.pdb -constraints::cst_file ca.ca.dist.cst -ddg::mut_file example.mut -ddg::iterations 50
#example.mut is a simple mutation, for instance a Leu to Ala mutation on res 1
L 1 A
As output I get a mut_L1A.out file containing 50*4 binary files in it, which I extract with the extract_pdbs protocol:
However I'm unsure if these (the 4 structures for every iteration from the 4 mpi job requests) are independent trials. I've compared the pdbs and they are the same - but the ddg_monomer iterations always converge so far. (all iterations for .pdb _1.pdb _2.pdb and _3.pdb files).
I suspect I should be able to find out from the random seed information in the log file... but I don't know how to make sense of it since it seems like there is more than one random seed number per structures.