[gmx-users] can anyone plx help me with the problem Listed nonbonded interaction between particles 112 and 120 at distance 3f which is larger than the table limit 3f nm.

[Justin Lemkul]

On 3/22/17 6:00 AM, Rapunzel Eugene wrote:
> I am trying to simulate a protein-ligand interaction. but my mdrun produces this error while running on command:gmx mdrun -v -deffnm em
>
> am getting the following error:
>  Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =        50000
>
> WARNING: Listed nonbonded interaction between particles 112 and 120
> 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.
>
>
>
> WARNING: Listed nonbonded interaction between particles 1889 and 1906
> 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.
>
>
> Step=    0, Dmax= 1.0e-02 nm, Epot=         -nan Fmax= 6.06156e+13, atom= 3
>
> I will be thankful for your suggestions. Thanking you in advance
>

You have severe atomic overlap or a broken topology.  See

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


and any of the million or so posts in the mailing list archive that deal with 
this same problem.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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