How can I build the wyoming like montmorillonite unit cell in avogadro for a molecular dynamics simulation? I am trying to build a unit cell for Wyoming-like montmorillonite, using Avogadro software. I am not sure how can I get access to the atom coordination and how to generate the .xyz file at the end? Is there any file that I can use as guidance during this process? Actually, I would appreciate any suggestions in this regard? please do not hesitate to share your knowledge with me.
I would suggest you try and find the unit cell (.cif file) of the compound in question from the CCDC database, and then use Mercury (a free version is available at the CCDC website) to create the system.
You can of course use Avogadro if that is what you like, but in my experience the coordinate files it produces for super cells are quite messy.