[gmx-users] Visualizing non-rectangular boxes

Ignacio Fernández Galván jellby at yahoo.com
Mon Oct 15 12:14:03 CEST 2007

Hi all,

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?


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