Honestly I don't think its possible to have a free software to do that simulation,but you can always use COMSOL Multiphysics for quick simulation with 30 days trial. 

If you need full physical detail, there is always geant4 and similar simulation engines from particle and nuclear physics, that are quite suitable for the purpose.

I think you can use some codes in FORTRAN like RAN3.

Try IbSimu  http://ibsimu.sourceforge.net/

Hi.

Perhaps it would be better to specify the context in which you want to solve the problem.  In high-energy physics there are opensource software frameworks for simulating collision processes and propagation of any sort of particle through vacuum and matter.  For example, Geant4 is a well-known C++ framework developed at CERN, which can be well interfaced with ROOT for visualization, storage, and data analysis, another opensource software from CERN.  On the other hand, if you want to trace ions propagating through the Galaxy and interacting (spallation process) with the interstellar medium (mostly protons), then you may prefer to look at what has been produced by the cosmic-ray community (GALPROP is a well known numerical approach, but there are alternatives that use semi-analytic computation of the diffusion equation).  Another possibility is ion interaction with the upper atmosphere, in which case the cosmic-ray community is still your place to look at, although this time you need to search for shower development.

BTW, if you only need to trace it through magnetic and electric field, you can solve the problem directly :-)  The trick is to get the equation of motion and pick any existing opensource software for solving the differential equation.  As there are no interactions in this case, using the packages above might look like overkilling.

Best regards,

Diego

you can try corsika and root

Go to the following link:

http://ibsimu.sourceforge.net/tutorial.html

IBSimu is a free code, which works as a C++ library. It's a particle tracking code with plasma simulation capabilities. A specific user-developed program written in C++ then performs each simulation. The user must be familiar with the C++ language. In return, the user can replace the built-in modules.