[gmx-users] REMD problem

Liu, Liang liu4gre at gmail.com
Thu Sep 29 18:42:12 CEST 2011

After running for more than 12 hours, the REMD simulation is completed and
what I get is 50 log, 50 trr, 50 cpt and 50 tpr files.
Not sure if the result is reasonable.

I tried to analyze the result, and after applying demux.pl, two
files replica_index.xvg  replica_temp.xvg are obtained.

My question is how to obtain the structure information? (I will need pdb

On Thu, Sep 29, 2011 at 6:23 AM, Manuel Prinz <manuel at pinguinkiste.de>wrote:

> Am Do, 29.09.2011, 01:38 schrieb Mark Abraham:
> > If the MPI configuration allows physical processors to be
> > over-allocated, then GROMACS is none the wiser.
> Over-allocation is the default in Open MPI[1]. So it's technically
> possible to run 50 MPI processes on 2 cores. Whether or not this is a good
> idea is left on as an exercise to the reader. ;)
> Best regards,
> Manuel
> [1] When not run from a resource manager that takes care of setting the
> "right" configuration options.
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Liang Liu
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