[gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT

[Justin Lemkul]

On 7/14/14, 9:38 AM, vivek sinha wrote:
> Hi Justin,
> I dont have the periodic molecules so do I include anything in the .mdp
> file? Also when I grompp this I get no warning or error or note. But when I
> mdrun it, I get
>
> WARNING: Listed nonbonded interaction between particles 35 and 114
> 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.
>
> and then the program terminates after displaying a segmentation fault error.
>
> Please provide any valuable suggestions.
>

Your system is blowing up.  It's a hard situation to diagnose with limited 
information, but something is almost certainly wrong with your topology.

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

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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 | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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