for free? chemical or nuclear simulators.
What kind 'simulator' are you talking about? What are you trying to do?
I want to put a Hydrogen atom next to a Helium atom, and give them initial velocities then see what happens in realtime.
You want a simulator in which you can smash the particles together or something?
The difficulty in such a simulator lies mainly in the communication between two parts: the simulation machinery, which is likely to need quantum mechanics, and the simulation visualization, which is not capable of "displaying" quantum-mechanical results.
The only thing I know of is GSIM built off GEANT. But it will only give you particle tracks and energy deposits. The other thing is you have to use electrons or real photons for beam particles and something as your target particle. These programs are pretty complicated if you don't have some one to help with some of the programming. You also have to program your target into the simulator. The detector also has to be designed unless you use one already available. But this is usually only for nuclear and particle physics.
Besides, depending on the momenta of the particles you are talking about will cause major hadronic showers. Just look at RHIC.
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