[gmx-users] Problem with Group and Verlet cut -off scheme

[Justin Lemkul]

On 7/8/16 1:01 PM, Ben Tam wrote:
> To follow on with that I have another question, this is the error I am keep getting when I turn on pressure couple (and now too with pressure couple off) :
>
>
> WARNING: Listed nonbonded interaction between particles 41 and 133
> at distance 4.169 which is larger than the table limit 2.000 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.
>
> The question means, does this mean my force field is not good or my crystal topology is not great? I convert my crystal file (.cif) by converting it to (.pdb) and using x2top function to convert it to .top file.
>

Unstable topology or inappropriate run settings.  See, e.g. 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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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