Over the past 40 years, computer simulations have become a useful tool for the study of biomolecular systems in a broad range of topics, including protein folding and binding equilibria and the study of enzymes, ion channels, and disordered proteins. By connecting the structure and energy of atoms and molecules, simulations mimic the dynamics of molecular systems across time scales over which many interesting biomolecular events occur. These molecular cartoons provide information difficult to access experimentally with full atomistic detail. This course is designed as a workshop with short introductory lectures and hands-on applications. The students will set up, conduct, and analyze molecular dynamics simulations on a topic chosen by the coordinator. Students will have the opportunity to contribute to a research project in collaboration with graduate students from the Pomès lab. At the end of this course, the students will have the skills to perform simulations on a protein of their choice.