[gmx-users] Visualizing non-rectangular boxes

[sebastien santini]

Hello,
I think you should use:

editconf -f config.gro -o config.pdb -visbox 1 1 1

donot forget to remove the
MODEL 1
and
ENDMDL

from the file if you want to see the box with pymol.

it works fine for me

SEB.


Ignacio Fernández Galván a écrit :
> 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?
>
> Thanks
> Ignacio
>
>
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 Sébastien SANTINI, PhD
 
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