[gmx-users] Visualizing non-rectangular boxes

[chris.neale at utoronto.ca]

> I'm trying to set up a simulation with a rhombic dodecahedron cell
> shape, for that I use editconf with the "-bt dodecahedron" option. Now
> I'd like to visually check the system configuration with a program such
> as VMD, but when I open the .gro files, I see the equivalent
> rectangular box used in the simulation (I guess). How can I generate a
> configuration file (.gro, .pdb, .trr...) with the dodecahedron shape? I
> tried with:
>
> trjconv -ur compact -s topol.tpr -f config.gro -o filenew.pdb
>
> but when I open filenew.pdb with VMD I still see the rectangular box.
> Am I missing anything?

Your trjconv command seems fine. Is config.gro actually a dodecahedron?
$tail -1 config.gro

Does it look like a dodecahedron?
    3.02251   3.02251   2.13022   0.00000   0.00000   0.00000    
0.00000   1.51125   1.51125

Or does it look more rectanguar?
   18.84582  18.63005  22.03044