This course is designed to provide comprehensive guidance on the preparation and setup of molecular dynamics simulations using CHARMM Graphical User Interface (GUI) and various simulation software platforms such as GROMACS, Amber, and NAMD. Participants will delve into the fundamental principles and techniques involved in setting up molecular dynamics simulations, including system preparation, parameterization, solvation, and equilibration. Through hands-on practical sessions and theoretical lectures, participants will gain proficiency in utilizing CHARMM GUI and different simulation software packages to construct and optimize molecular systems for simulations. The curriculum will cover essential aspects of force field selection, system setup, energy minimization, equilibration protocols, and analysis of simulation trajectories. By the end of the course, participants will acquire the necessary skills to prepare and conduct molecular dynamics simulations using diverse software tools, empowering them to explore molecular behavior and interactions in various biological and chemical systems.