It appears Molecular Workbench is open source as well.
We recommend that the Eclipse IDE be used to get the source code. You can access it through using SVN. Once you connect to our SVN server, check out trunk/common/java/simulations/mw/. The source code can also be browsed online.

Question on EJS and Molecular Workbench:
Can EJS be used to view

1. their implementation?
2. their java files be added to library of EJS ?

Question about Molecular Workbench
I don't understand their project enough to comment precisely, but
how to I see the equations that make this work?