[gmx-users] Box dimension size errors in MARTINI soft core simulation

[Justin Lemkul]

On 7/24/13 4:33 PM, Scott Pendley wrote:
> I am fairly new to gromacs and I am trying to run a thermodynamic
> integration simulation of a ligand disappearing in a box of octanol at a
> single set lambda point.  I have previous successful nvt and npt runs of
> this system.  When I have added the free energy portions to the input file,
> I get the following error:
>
> Fatal error:
> One of the box vectors has become shorter than twice the cut-off length or
> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> This seems unusual.  The box dimensions are 9.45 nm x 9.45 x 9.45 nm so
> that is fairly large even accounting for some shrinkage with a disappearing
> ligand.
>

The available information suggests the system has become unstable and is 
imploding.  See general troubleshooting information at 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System.

> Cutoffs in the input file are set as follows: rlist =1.4, rvdw=1.2,
> rcoulomb=1.2.  Doubling any of them would still be less than 3 nm which is
> significantly smaller than the box size.  Is there anything I am missing or
> any suggestions that others can give me?
>

I wouldn't mess with the cutoffs; they're an essential part of the force field. 
  For further diagnostics, please consider the points above and provide your 
.mdp file and Gromacs version.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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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