[gmx-users] editconf and genbox using method

Mark Abraham mark.abraham at anu.edu.au
Mon Mar 9 12:00:16 CET 2009

----- 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.


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