My simulation code seems to be working pretty solidly now and I've gotten almost my entire polyethylene model working. As of right now, I haven't addressed bond eclipsing and some of my interaction constants are a little off but, otherwise, everything seems qualitatively good.
Right now I've got my computer running a single C100H202 molecule at 273K. I am performing calculations for every femtosecond, recording for every picosecond and it will generate a full nanosecond in about 4 hours. After the calculations are done, I'll render up images and make a movie, which I will probably then post somewhere.
I'm a little disappointed in the state of the computation engine but I don't care; I'm just so glad that I got the model working.
UPDATE: It all worked out reasonably well and I have a video up on the page that I just made up for my thesis. Sadly, initial conditions and physics caused the system to develop a rotational mode that, combined with some software limitations, makes most of the video rather uninteresting. The first few seconds are nice. Further things will be placed on that site as they appear and will, for the most part, not be mentioned here.