Scripts for 
1. Creating files for MD simulations (generally NAMD, though modifications could build other setup files), 
2. Launching jobs on quest (generally with NAMD), 
3. Processing NAMD data (generally with matlab).

Setup scripts are a mix of shell scripts, vmd tcl functions, and a few perl one-liners or scripts.

Version tracking is done with git.

Currently, the main git branch is being rewritten in a cleaner manner.
A working system is in another repository.
Gradually, I am cleaning up and porting portions of the working repository to this one.