[gmx-users] The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

[Justin Lemkul]

On 3/15/16 12:23 PM, Poncho Arvayo Zatarain wrote:
> Hello, i ḿ working in a lipid bilayer using charmm36 forcefield and trying to
> do NVT equilibration but when i use grompp for nvt i receive the folowing
> error:  The cut-off length is longer than half the shortest box vector or
> longer than the smallest box diagonal element. Increase the box size or
> decrease rlist. I read about this at Manual of Gromacs and decrease the rlist
> but the error is still there. The other solution is to increase the box size
> but, it is safe to do this? or what can i do? i can attach my nvt.mdp file if
> you wantThanks
>

Cutoffs are an intrinsic part of the force field, so your box must be large 
enough to avoid minimum image violations.  Any reasonable lipid bilayer should 
be in a box large enough that no issues should arise.

-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 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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