Thank you very much. Trjconv works fine. Marian
On Mon, Mar 9, 2009 at 1:10 PM, Justin A. Lemkul <jalem...@vt.edu> 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 >> >> > -- > ======================================== > > 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 > > ======================================== > > _______________________________________________ > 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 >
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