Question about removing substrate for STM simulation

[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