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

[Berk Hess]

I just checked the 3.3.1 source code in md.c and the box is copied
from the xtc file.
I don't know where your problems could come from.

Berk.


>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] mdrun -rerun and box size bug not fixed?
>Date: Thu, 1 Nov 2007 06:12:56 -0700
>
>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.
>
>Thanks,
>David
>
>
>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
> > ==========================================================
> >
> >
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