I'm starting to code my own particles systems with python for blender. Where I can control substep and self-collision. This is my first test where I integrate verlet formula , simple inelastic collision and simple inelastic self-collision. For now it's take too much time to simulate because I need to integrate a kind of octree to avoid calculate distance between to far particles. But it's not too bad: Stats: 500 molecules Simulation time: 0.5sec per frame Substep : 5 substep per frame Number of frame: 360 (24fps) Render Time: ~1-2per frame blenderartists.org
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