[gmx-users] editconf and genbox using method

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 9 12:10:13 CET 2009

Mark Abraham wrote:
> ----- Original Message -----
> From: Nuno Azoia <nazoia at det.uminho.pt>
> Date: Monday, March 9, 2009 21:52
> Subject: Re: [gmx-users] editconf and genbox using method
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Hello!
>> Your box isn't rectangular. Your problem is just VMD display the gro
>> file with a rectangular shape. If you need to see your system properly
>> try to transform your .gro file in a .pdb file first, using trjconv.
>> Try trjconv -h to see the options
> I don't believe this is correct. That would be a bizarre thing for VMD to do. Much more likely is that editconf actually selected a rectangular box, genbox filled it, and VMD is displaying what's in the file.

Actually, I've found trjconv to be necessary.  VMD indeed shows a rectangular 
box for my dodecahedral systems, if I have not used trjconv -pbc mol -ur compact.

The transformation to .pdb, however, is unnecessary.  The .gro file can be 
processed in the same way.


> Mark
> _______________________________________________
> 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


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list