[gmx-users] Problem - can't set dodecahedrons box

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 9 02:16:34 CET 2010

Maurício Menegatti Rigo wrote:
> Hi,
> I'm facing a problem with GROMACS that appears pretty simple, actually. 
> I'm trying to set a dodecahedron box but all I can get is a triclinic 
> box. For that, I'm using the following line:
> /
> editconf -f pMHC -bt dodecahedron -o -d 1 /
> Am I doing something wrong?? Another problem, different from this one, 

There is no problem.  Whatever visualization software you're using is assembling 
the box as a triclinic representation.  You can post-process your trajectory 
using "trjconv -pbc mol -ur compact" to see the real representation.

> is that my protein, during the simulation, is escaping/comming 
> off/"running away" (sorry I'm butchering the english) from the water 
> box. I tried to use periodic boundaries conditions, but didn't work (I 
> added a line in my .mdp file - pbc = xyz). Someone could help me with 
> that, please?

Your protein is also not coming out of the box; it is a normal consequences of 
periodicity (which is, in fact, working just fine):



> I really appreciate !
> -- 
> Maurício Menegatti Rigo
> Núcleo de Bioinformática do Laboratório de Imunogenética
> Departamento de Genética
> Instituto de Biociências
> Universidade Federal do Rio Grande do Sul - Brazil


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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