[gmx-users] Gromacs and graphene sheets

Justin Lemkul jalemkul at vt.edu
Wed Jul 16 17:03:36 CEST 2014

On 7/16/14, 10:58 AM, Timothy Click wrote:
> I added the -alldih, readjusted the parameters to match the desired distances, etc., and if I don’t freeze anything, I receive the following error upon a minimization attempt.
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> There were 4490 inconsistent shifts. Check your topology
> WARNING: Listed nonbonded interaction between particles 6 and 48
> 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.

There's something fundamentally wrong, but I'd be guessing at what that is at 
this point.  If you package up your (1) coordinates, (2) topology (.top and any 
necessary .itp files), (3) force field files, and (4) .mdp files into a tarball 
and post them somewhere for download, I will take a look at this later today.



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


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