Dear El-Habed,
I am not quite sure what you mean with "sandwiched" and what plane you
want the molecule to lie in, but one tool you might want to look at is
gdis. It's a viewer that can read and write fdf files. You can select
your molecule in the gap and rotate (ctrl-right-mousebutton) or
translate (ctrl-middle-mousebutton). For more precise transformations
you can create rotation matrices and translation vectors in the (Tools
-> Building -> Editing menu (Transformations tab). On Ubuntu-based
Linuxes you can just install it with apt-get from the usual repositories.
Good luck,
Herbert
On 30/04/2019 09:31, 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
