Please use a descriptive subject line to help everybody. I suspect your use editconf is your problem. -princ may not preserve your box the way you've assumed. Try -princ -c, or editconf -princ then editconf -c.
It's also pointless and error-prone to compile MPI versions of the GROMACS tools. Only mdrun is MPI-aware, and the installation guides make this clear. Mark ----- Original Message ----- From: Ricardo Cuya Guizado <rcu...@hotmail.com> Date: Wednesday, May 19, 2010 4:14 Subject: [gmx-users] RE: gmx-users Digest, Vol 73, Issue 109 To: gmx-users@gromacs.org <!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size: 10pt; font-family:Verdana } --> ----------------------------------------------------------- | > Dear Friends I tried to obtain the XY density maps of the heme using g_densmap tool. The molecule was centered in the box The system was rotated to maintain the XY plane on the molecular plane. In the reference gro file, the molecule was also centered and the plane XY was on the molecular plane. To create the reference gro file editconf_mpi_d -f heme.gro -c -o heme_centered.gro -n index.ndx -princ To center the molecule in the box trjconv_mpi_d -f md10ns_heme.xtc -o md10ns_heme_centered.xtc -n index.ndx -s dmpr.tpr -center -boxcenter rect -pbc atom Rotations and translations were eliminated and the XY axis on the XY molecular plane trjconv_mpi_d -f md10ns_heme_centered.xtc -o md10ns_heme_centrado_centered_rottrans.xtc -n index.ndx -s heme_centered.gro -fit rot+trans To obtain the XY density map g_densmap_d -f md10ns_heme_centrado_centered_rottrans.xtc -s heme_centered.gro -n index.ndx -o densmap.xpm The result show the molecule in the corner of the figure and a diffuse withe region around the molecule. > > I will expect a more defined region around the molecule and centered. I need help, thanks Regards Ricardo ----------------------------------------------------------- > Gagnez 10 000 $ avec Hotmail! Participez ici | ----------------------------------------------------------- > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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://lists.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