Aspiring nanotechers and nanotechesses may want to look at the current Scientific American Amateur Scientist column, available online at http://www.sciam.com/1999/1099issue/1099amsci.html. If you follow the links at the bottom you can download a special demo version of a pretty nifty-sounding molecular modelling program from Stark Designs. Here is an excerpt from the article:
But Molecular Dynamics takes this all to a new level. It allows you to conduct an impressive array of virtual experiments to see how different atoms interact under all kinds of conditions. The program consists of numerous modules that demonstrate diffusion, osmotic pressure, the relation between temperature and pressure, the distribution of molecular speeds in a gas and many other topics. And you can use the software to discover things that even the most mathematically gifted physicist would be hard-pressed to wrestle from the basic theory.
The simulation runs so fast that when I first saw it at a conference I was certain it was a trick. The presenter put about 50 each of four different kinds of electrically neutral atoms inside a three-dimensional volume. The particle positions updated so quickly that I thought it had to be a computer movie, not a real-time simulation. So I decided to challenge the fellow.
In nature even neutral atoms can bond together. The mutual repulsion of the orbital electrons polarizes the atoms, and it turns out there is a range of distances over which these polarized atoms are attracted. So I asked the presenter to add these electrostatic interactions and then slowly decrease the temperature. He did. The heavier atoms began clumping together while the lighter ones kept speeding about, just as they should. He then rapidly brought the temperature to zero. The free atoms settled into small isolated clumps, again just as they should. That made me a believer.
I just downloaded the software but haven't tried it yet. It apparently has a number of "modules" that run specific simulations. I don't think you can create arbitrary scenarios with the demo software (no Drexlerian nanosynthesis modules yet probably). But it sounds like it might be fun.