Wow, that would be amazing.
I've often thought about the easy change it would be to make the Gravity Simulator work for Electricity. With a bit of extension, I could even see it working for all of Electromagnetism.
But modeling atoms, molecules and chemistry? That sounds like a tough job! To have a simulator that knew that H2O had a bonding angle of 104.5 degrees... and then when you changed the strength of the electric force slightly it could recalculate the new bond angle/length/vibrations... whew! And then it did that for ever conceivable (and unconceivable) arrangement of atoms!! I get the sense that a Nobel prize might be in the works for such an impressive simulator
But I may be going a bit overboard.
Here are a few tiers that I could envision:
1) Electricity! Yay - unlike the objects in the gravity simulator, we now have attraction and repulsion (... without resorting to negative masses or weird force laws, of course.) Could be nice and instructive, and fun to play with.
2) Electromagnetism. Kind of like the electric shocktopus, but just a sandbox for particles. And if you wiggled a charged particle, it would give off light. Sounds pretty cool, if a bit confusing to look at (picture all the field lines you'd need to understand how a light wave formed!)
3) 'Fake' Chemistry - In theory, with just electricity, we might be able to get some fake chemistry going on. Kind of like In Bond Breaker, say, where different particles attract or repel depending on how many 'electrons' are around their nucleus. This would probably not reflect the real world all that well, though... since for one thing many molecules are distinctly not 2D (think CH4), and I bet I'd have to leave out enough that some really strange stuff could happen. But it could certainly be a fun sandbox.
4) Real Chemistry - accurate virtual models... based on full quantum mechanical properties. I'll need a team of scientists and a decade.
5) Life - after millions of compute cycles, the molecules self-replicate, and grow into cellular and eventually multi-cellular life. I am their ruler.
Hm, I got a bit carried away.
Anyway, was one of those tiers what you had in mind? Or were you picturing something different?