[CP2K-user] [CP2K:18810] monitoring local structure upon qmmm meta

Victor Volkov volkovskr at gmail.com
Sun May 14 12:43:09 UTC 2023

 Dear users
I wish to post a question concerning  

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 
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.


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