The project is called Molecular Dynamics Studio. (yeah everything is a studio today)
The software is very alpha and so is the documentation. I hope to improve the software
over the next three years here at the University of Denver and want to especially add
static and dynamic cross-linking.
https://sourceforge.net/projects/moleculardynami/
If anyone is interested in sending wish-list features and/or interested in software development
on this open source project please contact me through the project. Suggestions are very welcome
and encouraged.