Molecular Workbench

The educational technology and digital learning wiki
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.


The term Molecular Workbench has three distinct uses. It refers to an open source molecular dynamics engine developed for use in education, to a lesson authoring system that creates student learning activities based on the engine, and to a series of NSF-funded projects at the Concord Consortium which produced the software. A searchable database of Molecular Workbench learning activites contains over 200 entries that are freely available under the Creative Commons non-commercial license.

“The Molecular Workbench (MW) 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.” ( Molecular Workbench retrieved 19:06, 21 July 2006 (MEST). )

The MW engine includes several unusual capabilities that make it useful in explaining and exploring chemical reactions, self-assembly in biological and nano-science systems, and light-matter interactions. The authoring environment supports the creation of simplified user interfaces, a variety of outputs, html text, and student assessments. 3D molecular visualizations can be placed on a MW page and then navigated to explore the shape and interactions in a complex molecule. Basic authoring is WYSIWYG based on a word-processor, but there is also a complete scripting capacity for more sophisticated applications.

See also: microworlds, simulation, visualization, authoring environment.

“MW is based on rigorous molecular dynamics calculations. Its simulation capacities and scientific accuracy are endorsed by calibrating simulations that self-prove scores of scientific laws. Scientists and engineers will find it useful in analyzing physical and chemical processes with simple, abstract models. Such models can be used to prove a concept, design a thought experiment, or serve as a prototype computational model before commiting to more concrete but usually time-consuming calculations involving considerable efforts. MW's revolutionary user interface enables users to quickly build a computational model, set up a simulation and immediately see the results while the simulation unfolds directly on the screen. Furthermore, when a simulation is saved, all the parameters, scripts, annotations and records also get saved in a format that can be loaded back in exactly the same original WYSIWYG form. You are absolutely freed from the burden of having to maintain numerous parameter-result sets in a traditional bookkeeping style.” ( Molecular Workbench retrieved 19:06, 21 July 2006 (MEST). )


Molecular Workbench is a special browser for opening model and simulation-based activities

The system runs under Java.


  • Java Web Start
  • Stand-alone


Molecular Workbench homepage (including downlowds)