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

Maurício Menegatti Rigo mauriciomr1985 at gmail.com
Tue Feb 9 02:12:46 CET 2010


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, 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?

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
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