Mark Abraham wrote:
----- Original Message -----
From: Nuno Azoia <naz...@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@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.
-Justin
Mark
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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