[gmx-users] error in minimization step

Justin Lemkul jalemkul at vt.edu
Thu Feb 23 13:18:25 CET 2017

On 2/23/17 5:05 AM, Kingsley Theras Primus Dass . wrote:
> Hello !!
> I am encountering an error in minimization step. Help me out to avoid this
> kind of error.
> The error message says,
> WARNING: Listed nonbonded interaction between particles 2999 and 3006
> At distance 2.442 which is larger than the table limit 2.400 nm.
> This is capable capable any
> A doubt molecule you are decoupling during a free energy calculation
> Since my inward beyond the table can not be computed,
> They are skipped until they are inside the table pricing again. You will
> Only see this message once, even if it too many rows.
> IMPORTANT: This should not happen in a stable simulation, so there is
> Something 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 19: Water matter starting at atom 63060 can not be settled.
> Check for bad contacts and / or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates

Your system is unstable.  Check the input coordinates carefully (note that mdrun 
tells you where the problem is!) and work from there.



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


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