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Is it possible to restart the ddg_monomer.linuxgccrelease?

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Is it possible to restart the ddg_monomer.linuxgccrelease?

Dear friends,
I am trying to use “ddg_monomer.linuxgccrelease” in our university cluster.
However, since my protein is too large (a dimer, each monomer contains 663 residues), the calculation ends because of the wall-time (72 hours) before it finishes.
I am here to ask if it is possible to restart the program. Or is there a method to make the program faster, like using MPI?  


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Mon, 2015-09-07 03:46

I don't see any indication of checkpointing or restart behavior in the ddg_monomer application. Also, it doesn't look like there's any support for MPI.

The one thing I think would be possible would be to split out the mutations which you're testing into separate resfiles or mutfiles ( Given the range syntax of the resfile (, it shouldn't be too hard to put together a set of resfiles which break up the protein into appropriately sized segments. You can then launch multiple runs of the program, each focusing on a small section of the protein. You'd then need to combine the results after the fact.

Wed, 2015-09-09 12:01