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

[Justin A. Lemkul]

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):

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> 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
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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