[gmx-users] center of dodecahedron

[Justin Lemkul]

On 1/26/14, 3:07 AM, Mahboobeh Eslami wrote:
> hi GMX users
> i simulate protein ligand complex in dodecahedron box
> when i use following command
>
> editconf -f complex.pdb -o newbox.gro -bt dodecahedron -d 1.0 -c
> My complex is not located in the center of box,
>
> How do I put the complex  in the center of box?

It is in the center, you just have to wrap the unit cell correctly with trjconv 
to see it.  See numerous previous discussions on this topic.

-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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