[gmx-users] mdrun WARING and crash

L.Liu at utwente.nl L.Liu at utwente.nl
Wed Feb 27 15:43:52 CET 2013

Dear Justin,

Thank you for your reply. I have some other questions,

1) Is it allowed to set nrexcl=0 in topology file in order to make every coarse-grained particles interact with each.

2) If it is allowed, then in [pairs] section, do I need to list all the pairs? 
For example, a linear chain with 10 beads:
[ pairs ]
1 2
1 3
1 4
1 5
2 3
2 4
9 10

or it can recognize the 1-5 1-6 or above automatically.

Thanks a lot

Kind regards,

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Tuesday, February 26, 2013 6:05 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdrun WARING and crash

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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