[gmx-users] Debugging

[David van der Spoel]

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
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++