yes it is a computer simulation. I want to a add an aromatic molecule on the surface (Chlorobenzene) on an oxide surface (in my case Cu2O:(110) CuO termination. I want to do a PES diagram for when the molecule is parallel and when is slightly tilted to the surface and to modify the distance from the surface with few angstroms to the center of mass of molecule. Therefore I need to find a way to measure this distance (from the center of mass of the molecule to any point of the surface) - if possible a simple one. I hope I made myself understood.

Thank you. There is a good point in using the centroid of the aromatic ring. Indeed I have played around with the molecule moving it around the surface but the reference atom it was the bromine since it is the most probable to be adsorbed on the active center . Therefore I have taken into consideration this distance which is not ok if I want to make comparison between the system with flate lying molecule on the surface, respectivelly the tilt position. Do you recomend a special software or graphical interface with which these parameters can be established easely. So far I am using jmol - but at a beginner level. I have to dig to find the way to determine these distances accuratelly.

Thank you

I the distance corrections considering the centroid of the aromatic ring and the PES of the two orientations almost superpose. Thanks for your suggestion