[gmx-users] Unstable System

[Justin Lemkul]

On 10/10/13 10:21 AM, Nikhil Agrawal wrote:
> DearAll,
>
> when I am running NVT equilibration phase i am getting following error
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.4#
> Wrote pdb files with previous and current coordinates
> starting mdrun 'Gromacs Runs On Most of All Computer Systems in water'
> 250000 steps,    500.0 ps.
>
> WARNING: Listed nonbonded interaction between particles 6483 and 6507
> 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.
>
> if any one have solution for that. please let me know
>

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

You haven't told us what your system is, what force field you're using, or what 
prior preparation steps you have done (energy minimization and its outcome). 
Without vastly more information, no one can help you very effectively.  These 
sorts of problems are posted to this list almost daily, so please spend some 
time in the list archive.  There is certainly something helpful among the 
thousands of posts describing unstable systems and blowing up.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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