[gmx-users] Unstable System
devicerandom at gmail.com
Thu Oct 10 18:37:26 CEST 2013
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:
>> 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
> 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 A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
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