[gmx-users] Protein is not at the centre of octahedron box

Justin A. Lemkul jalemkul at vt.edu
Thu May 14 14:13:24 CEST 2009

sukesh chandra gain wrote:
> Dear All,
> I am doing a simulation for ligand-enzyme complex in a octahedron box. I 
> have mentioned -c with editconf, but after energy minimization the 
> protein is placed at the top of the box. Could you please suggest me how 
> could I keep the protein at the centre of the octahedron box?

This is simply a visualization artifact.  Use trjconv -pbc mol -ur compact to 
"correct" your structure.  But do be aware that this is simply a convenience for 
visualization, in an infinite system (with PBC), there is no "center" of a box.


> Here are the details:
> After
> editconf>
> Volume =283.195nm^3
> System size : 6.852 5.060 7.638
> genbex>
> box_margin = 0.315
> Removed 29370 atoms that were outside the box
> grompp>
> Using a fourier grid of 88x88x88, spacing 0.115 0.115 0.115
> Thank You,
> Regards,
> Sukesh
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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