Dear gmx users I would like to simulate a system: carbon nanotube+some small molecules. first I want to align CNT along the z direction. to do that I used the commands: editconf -f cnt.pdb -o cnt.gro -princ -box 5 5 5 editconf -f cnt.gro -o nano.gro -rotate 0 90 0 and then I used genbox: genbox -cp nano.gro -ci smallmolecule.pdb -nmol 24 -o out.gro but when I looked at the out.gro in VMD I saw that the orientation of my carbon nanotube has changed slightly.would you please tell me how I can fix that? Best regards
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
