The Molecular Workbench software is a free, open-source modeling and authoring program specifically designed for use in science education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and 3D, it provides a simulation platform for teaching and learning science through atomic-scale reasoning. Many important concepts in physics, chemistry and biology that are otherwise too abstract to understand can be visualized with dynamical and interactive simulations. You can also find out some existing activities at the MOLO and MOLIT curriculum databases.
Java 5.0+ is required to run the software. For Windows and Linux users, please go to http://java.com to install Java. For Mac OS X users, make sure that the latest Java version is installed. Once you have Java, just click on the MW2.jnlp on this site to launch the software.