[gmx-users] Debugging

[Kirill Titievsky]

Erik,
> 0. What Gromacs version, hardware, and operating system version are you
> using?  
I'm using the current version of GMX posted on the website running
under Linux Kernel 2.6 on an  P4.
> 1. By "stop running", do you mean crash, or a freeze where the step
> count stops updating?
That's exactly it: simulations just stop running.  No error messages,
md.log stops in the middle of a line.

Does this give any clues?

thanks

> 2. If it is a Mac (using Altivec) or x86 (using SSE/SSE2/3DNow), try
> disabling assembly loop support by setting the environment variable
> NOASSEMBLYLOOPS (to anything) before starting mdrun.
> 
> Cheers,
> 
> Erik
> 
> On Feb 17, 2005, at 2:00 PM, 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.
> >
> >
> > Many thanks
> >
> > Kirill Titievsky
> > Chemical Engineering
> > MIT
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> 
> 
>