[gmx-users] Unstable System

[massimo sandal]

Taking a shot in the dark, when it happens immediately like that (step0) in
my experience it often means the topology is wrong.
On 10 Oct 2013 16:27, "Justin Lemkul" <jalemkul at vt.edu> wrote:

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