@Justin Lee, I'm not familiar with Berkley Madonna and I bet most other readers aren;t. If you post the equations you are trying to simulate, instead of a bunch of code that people cannot parse, you will be more likely to get a helpful reply.
You can format your equations by clicking the capital sigma icon about the message window. The equation editing window which pops up uses Latex formatting. I always thought Latex was too complicated for me, but I finally gave it a try a week ago, and it is easier than I expected. Every time I want to do something, I do a google search: "Latex for subscript", "Latex for a fraction", etc. Example (I think this is one of your differential equations):
I recommend reading Intro to solving ODEs in Matlab and the Matlab help for ode45(). One of the things you will learn is that you don't need DT=0.02 (which your code defines) because ode45() is a 4th order Runge Kutta routine with adaptive stepsize - the routine figures out and adjusts the step size as it goes.
