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 Nuno Azoia On Mon, 2009-03-09 at 12:23 +0200, Marian Butu wrote: > Hi, > > I want to obtain a dodecahedron box to start a simulation of a small > peptide. But, even if I use dodecahedron option or octahedron, I > obtain a rectangular box. > > > > Gromacs version: 4.0.4 compiled on redhat server 5 (I do this after > 3.2.1 binaries for MS Windows) > > Command line that I used: > > pdb2gmx -f pep1.pdb -p pep1.top -o pep1.gro -water tip3p > > editconf -f pep1 -o -bt octahedron -d 0.3 -c > > genbox -cp out -cs -p pep1 -o pep1_em > > > > And, when I'm looking to pep1_em.gro with VMD the box is very very > rectangular. > > > > Please, somebody help me with this problem. > > > > PS. I'm a new user of Gromacs but I'm read all the messages from the > www.mail-archive.com/gmx-users@gromacs.org about this problem but I > still don't understand what I need to do to obtain the correct box. > > > > Thank you very much in advance for any suggestion. > > Marian > > > > > > _______________________________________________ > 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 _______________________________________________ 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
