In module eight, the students learned the concept of MD simulations. The instructor guided the students to use NAMD , a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems, to conduct energy minimization, heat the system, equilibrate the system, and perform the production run by providing the students a script. In addition, the VMD tool was used to solvate the protein in water and add ions to neutralize system charges. The students learned to complete these tasks by submitting their jobs to the HPC system and using NVIDIA V100 graphics processing units (GPUs) to accelerate the simulations.