Build custom OpenMM scripts right in the browser! OpenMM is one of the most flexible molecular dynamics packages, put it can be a little intimidating for the new user. Instead of interacting with it via a set of command line scripts, as one would with amber or gromacs, to interact with OpenMM you write a little python script. If you've never written a script before, this might seem a little unfamiliar, but it's an incredibly powerful paradigm.
But to help you out, I've written a little web application that'll build an OpenMM python script for you. As you select the options via the menus, the script will be "written" for you, live. The code is live on heroku, at builder.openmm.org, and free (GPL) on github. Fork away.
It would be really awesome if the webapp had a "run" button that would run your simulation for a short period of time on a donated GPU, but that's going to a little nontrivial, especially with the security ramifications. Pull requests welcome!