Performing MD simulations for antibodies and excipients and analyzing their binding sites are challenging, receiving scores closer to 3.5, which is still a learning experience but not to the desired extent. MD simulations are usually covered in graduate statistical thermodynamics courses or as elective courses. Therefore, in this project, the instructor prepared a script for students to perform MD simulations and analysis. Designing another module to introduce the basic statistical thermodynamics and go through the simulation setup and the analysis more clearly could enhance students' learning.