Dear El-Abed,
you can use Avogadro software (it is free) to rotate your molecule. The
easiest way would be to select molecule, then use option add center of
atoms,
a usually copy coordinates to Origin, move center of atoms to 0,0,0 then
return it to Avogadro, this step is because Avogardo rotates around
origin.
Kind regards,
Aleksandar
--
Aleksandar Tomovic
Institute of Physics Belgrade
Pregrevica 118, 11080 Belgrade, Serbia
http://www.ipb.ac.rs/
On 2019-04-30 10:31, El-abed Haidar wrote:
Good afternoon all,
I am trying to use a new molecule below:
and I would like sandwich it between the gold electrodes i have used
in before. Relaxing the whole structure together after long time did
not work. I have taken the alternative of relaxing the structure on
its own. Then sandwich it directly onto the gold electrodes.
My Problem is the molecule does not belong to the plane where it is
suppose to be sandwiched:
Both are in complete different positions. Does anyone know what one
can do in this case?
Any advice would be appreciated.
Thank you!
EL-Abed
El-abed Haidar | Doctor of Philosophy (Science)
Condensed Matter Theory (CMT) Group
| School of Physics
THE UNIVERSITY OF SYDNEY | NSW | 2006
