[gmx-users] Location of a molecule in a dodecahedron

[Justin A. Lemkul]

Birgit Hischenhuber wrote:
> Hi,
> 
>  
> 
> I simulate a molecule in a dodecahedron.
> 
> I used at the step with the editconf:
> 
>  
> 
> editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0
> 
>  
> 
> After my simulation I looked at the first frame and saw, that at two 
> direction the molecule is actually 2 nm away of my edge, but the at the 
> third edge the molecule is not in the middle, but near the edge.
> 
> I looked also at the other pdb-files with the water before the 
> simulation, and there the location of the molecule is the same, in my 
> opinion not in the middle of the body.
> 
>  
> 
> Is this a bug? Or have I done anything wrong?
> 
>  

There is no bug.  The representation is simply a triclinic cell, and probably 
periodicity effects.  For visualization purposes only, you can "correct" the 
representation with trjconv -pbc mol -ur compact.

-Justin

> 
> Thanks a lot for your helps!
> 
>  
> 
> Greets, Birgit
> 
>  
> 
> ---
> 
>  
> 
> DI Birgit Hischenhuber
> 
> Unit for Medical Statistics and Informatics
> 
> Section for Biomedical Computersimulation and Bioinformatics
> 
> Medical University of Vienna
> 
> General Hospital
> 
> Spitalgasse 23, BT88
> 
> A-1090 Vienna
> 
>  
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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