Using VMD, the earlier examined protein in PyMOL could be edited to stitch the protein chains together and mutate to the target sequences. Finally, the NAMD program was introduced to perform MD simulations of the antibody systems and analyze their interactions with excipients. Through the program, students acquire the necessary skill to apply molecular modeling and simulations for biologics design. Overall, the students have positive feedback on the learning objectives of understanding biopharmaceutical development, formulation designs, and molecular modeling of antibodies. MD simulations are challenging for the students; therefore, the instructors can spend more time introducing the fundamental theory of statistical thermodynamics in the revised curriculum. Furthermore, the software implemented in this program is free, which is advantageous to classes with a limited budget.