[gmx-users] Debugging

[Kirill Titievsky]

David, would a particle coordinate outside the box cause a crash?  I
definitely see that in the trajectories, although I'd expect the
boundary conditions part of the code to shift everything into the
primitive box.  I use soft potentials that guarantee that  forces are
finite no matter where the particles are.  Meanwhile, the code reports
infinite forces, making me think that unless this is a bug in the
tabulated potential part of the code, there is something wrong with
the way the closest image convention is applied.

thanks

On Thu, 17 Feb 2005 08:40:35 +0100, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> On Thu, 2005-02-17 at 08:00 -0500, Kirill Titievsky wrote:
> > Dear All,
> >
> > Gromacs seems to just stop running in the middle of half of my
> > simulations.  No error messages.  Where do I start debugging?  Is
> > there a debug reporting level in Gromacs?
> >
> > Symptoms:
> > The logs get cut off in the middle of a line.  It appears that this
> > has something to do with atoms ending up outside the box -- the
> > trajectory files show some files to be outside and restarting the
> > simulation shows NaN forces on some atoms, even though I'm using soft,
> > finite potentials.
> >
> Start by saving coordinates more often and/or look at the trajectory.
> Large forces can cause crashes in zillions of ways.
> >
> > Many thanks
> >
> > Kirill Titievsky
> > Chemical Engineering
> > MIT
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
>