[gmx-users] Debugging

Erik Lindahl lindahl at sbc.su.se
Thu Feb 17 20:08:25 CET 2005

Hi Kirill,

0. What Gromacs version, hardware, and operating system version are you 
1. By "stop running", do you mean crash, or a freeze where the step 
count stops updating?
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
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