[CP2K-user] [CP2K:14225] Re: Geometry optimisation of organic molecule on fcc Au(111) slab

[Anton Lytvynenko]

Dear Dmitrii,

in addition to the suggestions you've already received from Dr. 
Iannuzzi, I could append the following comments.

16.11.20 03:48, DMITRII Drugov пише:
> I expected organic molecule moves more from it's initial position. 
> Otherwise it's almost same as I built in avogadro software.

As far as I can see from your files, you have pre-optimized your system 
via MM(UFF) in Avogadro. The molecule actually "lays" on the surface 
(take a look on the structure in the "van der Waals spheres" mode in 
Avogadro). Bearing that in mind, I see no reasons to expect any 
significant movements in so heavily constrained system. You effectively 
allow only movements relevant to intramolecular interactions in your 
adsorbate and van der Waals interactions between the molecule and the 
surface -- both of them are reasonably well described within MM approach 
(due to the adsorbate structure, no specific covalent bonding between 
this molecule and the surface is to be expected).

> Do you think while optimization I should keep system non periodic with 
> poison wavelet  or periodic in xy or xyz with poison analytic?

You may want to consider this paper: Phys. Chem. Chem. Phys., 2018, 20, 
8456.

Yours,
Anton