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.
Nuno Azoia On Mon, 2009-03-09 at 07:10 -0400, Justin A. Lemkul wrote: > > 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 > > _______________________________________________ > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- Nuno Gonçalo Azoia Lopes Finishing Research Laboratory Textile Engineering Department Universidade do Minho Campus de Azurém 4800-058 Guimarães Portugal Tel: +351 253 510 280 - Ext: 517 289 Fax: +351 253 510 293 Mobile: +351 965 382 487 E-mail: naz...@det.uminho.pt _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
