[gmx-users] Visualizing non-rectangular boxes

sebastien santini santini.s at fsagx.ac.be
Mon Oct 15 15:05:15 CEST 2007

I think you should use:

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

donot forget to remove the

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

it works fine for me


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
>       ___________________________________________________________ 
> Want ideas for reducing your carbon footprint? Visit Yahoo! For Good  http://uk.promotions.yahoo.com/forgood/environment.html
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


 Sébastien SANTINI, PhD
 CBMN, Faculté Universitaire des Sciences Agronomiques  
 Passage des déportés, 2  
 B-5030 Gembloux, BELGIQUE

 GSM: 00 32 (0)4 98 59 53 65

More information about the gromacs.org_gmx-users mailing list