In recent years, physical chemistry students at Erskine College and the University of North Carolina at Chapel Hill have used the Virtual Substance program to learn thermodynamic concepts and practice authentic scientific research in the classroom. Virtual Substance is a molecular dynamics simulation program with a visualization component. Students can manipulate thermodynamic variables and interaction potentials to study the properties of gases, liquids, and solids. We have designed a variety of modules that help students connect the microscopic behavior of particles with their macroscopic physical properties as well the equations of state that connect them. Students have also completed independent research projects. The students develop skills using Virtual Substance that are critical in their growth as scientists. An overview of the program, modules, student results, and independent project topics will be presented.