[gmx-users] Lyzosyme with ligand tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 24 19:27:47 CEST 2011

James Starlight wrote:
> Justin, hello!
> I have forced with some problem during final stage of your turorial.
> I dont know why but after NPT phase my sytem has occured in the standart 
> cubic box instead of dodecahedron (after all previosly phases my system 
> was in correct box).
> So when I've passed my system in the MD stage- it's moved back into 
> normal dodecahedron box but on the placement where previously system 
> was. So as the consequence I've obtained protein in the wrong place ( 
> some of its parts were outside new box )
> I've tried examined why this might occur but have not found possible 
> explanations.
> I've examined box coordinates of the all .gro structurs obtained after 
> each of the stages and all of them contained such box vectors
> 7.85059   7.85059   5.55120   0.00000   0.00000   0.00000   0.00000   
> 3.92529   3.92529
> As I understood It's correspond to the system in the dodecahedron box 
> but my ntp.gro structure with the same is in the cubic box ( with the 
> above box coordinates as well). Why its might occured and were else 
> information of the box coordinates is present exept of initial structure 
> gro file ?

You still have a dodecahedral box.  The default representation is a simple 
triclinic cell.  A true compact representation can be obtained with:

trjconv -pbc mol -ur compact



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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