This course aims to enable the student to understand and predict properties of microscopic systems in materials science, physics, biology, and chemistry. We will cover the basics of molecular simulation methods, and provide an overview of modeling tools for problems of interest. In particular this course will cover both hard and soft matter materials spaces. The course is geared toward students with an interest in molecular modeling, with or without prior experience in the area. At the end of this course, students should have a general knowledge of current state-of-the-art molecular simulation methods, and be able to design, run, and analyze simulations for systems of interest.