It's still quite hard to do simulations on the timescales needed for any sort of interesting chemical reaction or physical effects. Foldit (http://fold.it/port

It's still quite hard to do simulations on the timescales needed for any sort of interesting chemical reaction or physical effects. Foldit (http://fold.it/portal/ http://fold.it/portal/) is probably the best there is – a game that actually contributes to the science of protein folding. You can also try GROMACS to actually run physical simulations, but it's more involved and not what you'd consider interactive. But you can look at your molecule wiggling in space with any pdb viewer.