kiroosha at gmail.com
Fri Feb 18 22:44:40 CET 2005
> 0. What Gromacs version, hardware, and operating system version are you
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?
> 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.
> 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
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