[gmx-users] Gromacs not writing checkpoint files with multidir/replex (v 4.6.4)

Mark Abraham mark.j.abraham at gmail.com
Tue Mar 25 23:57:34 CET 2014

That's the first I've heard of that. As a work-around, my experience with
4.5 was that mdrun -multi worked correctly with checkpoints, and so should
4.6. Please open an issue at http://redmine.gromacs.org, where you can
upload your files. (You can't attach things to mail to this mailing list.)


On Tue, Mar 25, 2014 at 6:00 PM, Michael Daily <mdaily.work at gmail.com>wrote:

> Hi all,
> I have been attempting to perform successive MD runs using the -multidir
> option, in conjunction with replica exchange, using restart from
> checkpoint.  The first time the run is performed (see the shell script), a
> checkpoint file is created in each of the 6 directories, as expected (see
> stderr output in run1.log).  The second time, the runs resume from the
> checkpoint files generated by the first cycle, BUT no new checkpoint files
> are generated (see run2.log).  Thus, when I attempt a third round, the
> simulations restart with the same checkpoints from the first cycle (see
> run3.log).  Thus, it is effectively impossible to resume multidir/replex
> simulations more than once.  Does anyone know of a fix for this problem, or
> will some more elaborate solution be required, such as manually
> daisy-chaining a set of short runs in separate directories?
> Thanks,
> Mike
> Additional notes:
> 1) gmx 4.5 has the same problem
> 1a) No problem occurs when trying to extend an individual one of these runs
> indefinitely without -multidir.
> 2) the problem occurs whenever using -multidir, not just if replex is used.
> 3) While I am using short -cpt intervals for testing purposes, the same
> problem occurs if the standard interval (15 min) is used.
> 4) Using -noappend doesn't make a difference
> --
> ====================================
> Michael D. Daily
> Postdoctoral research associate
> Pacific Northwest National Lab (PNNL)
> 509-375-4581
> --
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