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Perform MPI relax with movemap files

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Perform MPI relax with movemap files


I want to relax around 3K structures. Also, I have a movemap file for each of these structures. How do I trigger mpi runs for relax with movemap files?

Earlier, when I did not need the movemaps, I used the following command:

mpiexec -np 32 $ROSETTA/bin/relax.mpi.macosclangrelease -in:file:l <pdb list file> -nstruct 20

But, now I want to perform relax with move map associated with each of the pdb file in the pdb list file. How do I do it?

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Sun, 2017-03-05 13:18

Unfortunately, there currently isn't a way to map different input files (movemap files, resfiles, disulfide files, etc.) to different input structures. That's something that's actively being worked on, but it's not something that currently works.

Instead, I'd recommend setting up the "embarrassingly parallel" approach by launching individual (serial) jobs, one for each input structure/movemap combination. There's a number of utilities (such as GNU parallel) that make this easier for multi-core systems, so you're not manually managing job distribution. (To be honest, all MPI relax is doing is the equivalent of the GNU parallel command with the serial relax protocol.)

Mon, 2017-03-06 08:54

You can also look into JD0 in the tools directory.  It's a pair of wrapper scripts and documentation intended to make this kind of job easier.

Mon, 2017-03-06 08:59

Thanks guys. I had a similar idea as that recommended by rmoretti if there was no way of doing it. But I will look at JD0 as well. Thanks again.

Mon, 2017-03-06 10:03