[gmx-users] mdrun WARING and crash

[L.Liu at utwente.nl]

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,
Li

________________________________________
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.

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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