Hi all, I am new to LAMMPS. Is anybody working or have an idea on ion exchange or adsorption process using MD Simulation? I need guidance on how to create the simulation box for the adsorbent (Zeolites).
This link will be a useful place to start. 
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You need more help than that, and it is help you are not likely to find here. What you are asking about are questions that are usually discussed with an adviser or tutor. Nobody here has the time to be your adviser or tutor and this is not a forum meant for tutoring people in learning how to do MD simulation studies, this is a forum for resolving problems with the LAMMPS MD software.
That you want to use LAMMPS does not make your problems automatically LAMMPS problems. The bulk of what you need to learn is independent from LAMMPS and would apply to any simulation software.
I don’t know much about MD simulation studies of the kind of system you are asking about, but I know one thing: you are not likely to get useful results from MD simulations alone. The process you are studying is a complex, activated process and that makes it very difficult to study for the length and time scales available to atomistic MD simulations. You will need to run MC or a hybrid of MC and MD instead. How to set up your geometry and assign settings and parameters is the least of your worries.
That said, the way how you learn about this in science is that you look up relevant publications and also study text books. But most importantly, you need to find yourself a competent tutor/adviser. Don’t do this on your own, you will waste enormous amounts of time, make many errors that you don’t notice and will at best only produce barely acceptable results. That is because you are using a technology where there is most 60 years of experience in the published literature and thus a large amount of accumulated knowledge of what can be done and what (easy to make) mistakes must be avoided.
If you are new to LAMMPS I would also strongly recommend to learn and practice MD with some simpler problems (there is a whole bunch of tutorial materials available) and learn your basic simulation skills before attempting to simulate a complex system like you describe you want to work on.