Hello and greeting to everybody. I’m a begineer in simulation.
I’m working on a simulation of a system contain triethylene glycol and zif-8. I’m making teg fluid by packmol and have a pdb file of it but I have zif8 structure in cif format. How can I do a simulation with an interface of teg and zif-8? And how can I convert the cif format to pdb?
you do a simulation of your system like with any other system:
- get/construct an initial geometry in a format that LAMMPS can process or that can be converted correctly so LAMMPS can process it
- find a suitable force field and assign force field types and parameters
as you are a beginner, you should begin with something simpler and where the results are known, so you can compare what you did. there are tutorials, too.
as for converting a cif file, try searching the web.