[gmx-users] Launching Replica Exchange MD
mark.abraham at anu.edu.au
Tue Dec 19 07:09:18 CET 2006
> Hello everyone,
> I can't seem to find how to start a replica exchange MD job. I have a
> .tpr file for each replica. How do I give these to mdrun?
They need to be named remd0.tpr, remd1.tpr, remd2.tpr etc. Then mpirun -n
4 mdrun -np 4 -s remd will do the job. "man mdrun" has the details.
> Also, for
> purposes I wanted to run a few of my replicas on the same node (otherwise
> have to wait in a queue) just to make sure my acceptance ratio is what I
> it should be. Is this possible?
Sure, just grab a contiguous subset, copy them somewhere safe and run your
test job. Be aware that depending on your system, the acceptance ratio can
vary with temperature... see a JCTC paper (I think) from earlier this
year. So don't stress too much about matching up the acceptance ratio to
some pre-planned value.
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