[gmx-users] mdrun -rerun and box size bug not fixed?

David Mobley dmobley at gmail.com
Thu Nov 1 14:12:56 CET 2007

Dear Michel,

Are you sure you're using 3.3.1? I have not checked this specific
issue -- but I have checked that if I run hydration free energy
calculations in patched 3.3.0, and again in patched 3.3.1, and do my
usual free energy analysis using mdrun -rerun, I get the same values.
That either tells me that (a) the patch is in 3.3.1 also, or possibly
(b) that the problem is small enough for hydration free energies that
I'm missing it.

Anyway, hopefully (a) is true, otherwise I'm going to need to repeat a
LOT of work (and be very grumpy). Keep me posted on this.


On 11/1/07, Michel Cuendet <michel.cuendet at isb-sib.ch> wrote:
> Hi gromacs people,
> I was trying to rerun old xtc trajectories to recalculate some energies
> involving the solvent, using gmx 3.3.1. I saw important discrepancies
> with the original energies (nstlist=1, xtc unaccuracy tolerated). After
> some struggling, I figured out that the box size is determined form the
> .gro file used to create the .tpr file, and are not read from the
> trajectory. I then realized that this problem had been described two
> years ago on the list:
>     http://www.gromacs.org/pipermail/gmx-users/2005-October/017729.html
> The issue was then transferred to bugzilla :
>     http://bugzilla.gromacs.org/show_bug.cgi?id=26
> and a patched md.c was proposed by David, apparently for gromacs 3.3.0.
> It seems that this patch has not been integrated in gmx 3.3.1, because
> the -rerun option still gives wrong energies. What's worse, the patched
> md.c cannot be used for 3.3.1, because apparently the number of
> arguments for init_md() has changed.
> Could someone work out a patch for 3.3.1, and maybe post it on the same
> bugzilla thread?
> I think this bug should be mentioned in the "known bugs" section of the
> website. That would probably save some sweat to others like me trying to
> use the -rerun option...
> Thanks,
> Michel
> --
> ==========================================================
> Michel Cuendet, Ph.D
> Molecular Modeling Group
> Swiss Institute of Bioinformatics
> CH-1015 Lausanne, Switzerland
> www.isb-sib.ch/groups/Molecular_Modeling.htm
> ==========================================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list