[gmx-users] mdrun WARING and crash

Justin Lemkul jalemkul at vt.edu
Tue Feb 26 18:05:28 CET 2013

On 2/26/13 11:57 AM, L.Liu at utwente.nl wrote:
> Dear all,
> I got WARNING after mdrun, which says:
> "WARNING: Listed nonbonded interaction between particles 794 and 797
> at distance 3f which is larger than the table limit 3f nm.
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason."
> I don't quite understand the 'table limit 3f', what does it mean?

That's a simple output typo, though it's somewhat important.  The format is for 
a floating-point number, printed with 3 decimal places (%.3f).  For some reason 
that's not coming through correctly, though it did in previous versions.

> In our system, the bonded interactions is FENE, and the non-bonded LJ interactions are between every coarse-grained beads by setting nrexcl=0 in topology file.

There's some physical instability in the model that is causing the system to 
blow up.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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