Algodoo

This is a little boring to watch because it takes a long time before they begin to coalesce, but I found by moving the walls in closer (top, bottom, left, and right), then they coalesce much faster, and the scene then changes from being boring to being interesting!

Good job!

Hows this?

I do wish there was a way I could make the molexules change color depending on the forces exerted on it, And I also wish that I could make them form multiple bodies first, THAN, make the big balls. Its a thing with having walls, I guess.

What do you mean by "forces"? There are a few things that can be measured and the values used for other things, such as, linear velocity, angular velocity, X & Y position, acceleration, and maybe a couple of others. By scaling the measured value so that it covers the proper range of the colored geometry, you can have the colors become an indicator of the force.

By forces i mean how mcuh there being repeled by other molecules - Try freezing the velocities than leaving only 2 molecules in existance, They will come together, but when they get too close, they repel apart.