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I suspect that what you want to do is simply not possible in Geant4, or at least not possible with any accuracy (say, within a few orders of magnitude). But it's not clear to me what you are actually trying to do.
If you want to put a proton beam into a target and calculate the time-evolution of isotopes in the target, then Geant4 cannot do this with any accuracy -- you would need vastly more events than any supercomputer could simulate (because the trace elements can be important, even when they are only 1E-10 of the target). You will need a combination of programs, such as MCNP6 and CINDER, or KENO and ORIGEN, which are designed for this. It should be no surprise that these are nuclear physics codes, not HEP codes like Geant4.
If this is not what you are trying to do, then you need to be more explicit in your question.
A few more details:
MCNP6 and KENO are simulation codes related to Geant4 (but differing enormously in details). They simulate particle transport and can be used to calculate the neutron flux in the target (neutrons are by far the dominant particles that induce transmutations in most targets). Among many other things, these programs depend on the geometry and materials of the system. Note that MCNP6 can handle protons but KENO can not.
Once you have the neutron flux in the target, CINDER and ORIGEN solve the transmutation equations and compute the evolution over time of isotopes in the target. These programs depend on the materials and neutron flux, but not the geometry; they contain a vast library of which isotopes decay to which, and how neutron-induced reactions affect the nuclei. Note that as the isotopic composition of the target changes, so does the neutron flux (especially if fission is involved), so in practice one iterates between a pair of these programs, re-running the simulation code whenever the composition of the target changes enough to affect the flux.