[gmx-users] orientation of CNT

Abed Askari abedaskari at yahoo.com
Fri Aug 3 20:23:15 CEST 2012

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

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