[gmx-users] editconf and genbox using method
nazoia at det.uminho.pt
Mon Mar 9 12:29:20 CET 2009
Exactly. In my simulations with octahedron box I encounter the same
problem. I just transform it in pdb to use it with pymol, that's all.
But I have to use the same kind of options Justin use.
On Mon, 2009-03-09 at 07:10 -0400, Justin A. Lemkul wrote:
> 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
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Nuno Gonçalo Azoia Lopes
Finishing Research Laboratory
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