Molecular Workbench
Molecular Workbench is a site that allows users to create simulations for different topics. This tool can allow students to get a moving visual representation of the things they're learning in the classroom. It also allows users to create their own simulations. This could provide an opportunity for students to create their own simulations. However, I would recommend only older and/or more advanced students create their own simulations due to the steeper learning curve.
