[gmx-users] mdrun WARING and crash
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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users