monitoring local structure upon qmmm meta

[Victor Volkov]

Dear users

I wish to post a question concerning 

https://www.cp2k.org/howto:biochem_qmmm

In the section "Equilibration at MM level"

it is suggested to

" Visualize your simulation to check for any abnormalities."

Well, once incrd and prmtop files are written and after

cp2k prints coordinates in xyz format,

VMD (or or alike) don't distinguish to use select substructures of interests:

everything is imaged at once.

Of course, if atoms of interests are known, it is possible to write own code

(with Mathematics or alike) to visualize.

However, may be there is an industrious solution?

Would you comment?

Thank you.

Victor