[CP2K-user] [CP2K:22152] Question about substrate removal for STM simulations in cp2k

[Shravni]

Dear CP2K users,

​I am a beginner with CP2K and am currently working on STM simulations. 
I've been following the tutorial for simulating STM images of a graphene 
nanoribbon adsorbed on a metallic substrate, but I’m a bit confused by one 
step—it shows the metal substrate being removed from the system before the 
final calculation.

​Is it standard practice to run the simulation on the molecule alone? 
Wouldn't excluding the substrate significantly change the electronic 
structure and the resulting images? I’m wondering if I can get reliable 
results by simulating the molecule in isolation, or if I should keep the 
metal atoms in the cell.

​I would really appreciate any clarification or advice on this.

​Best regards,

​Shravni

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