Experiments in which ultra-cold neutral atoms and charged ions are overlapped, constitute a new field in atomic and molecular physics, with applications ranging from studying out-of-equilibrium dynamics to simulating quantum many-body systems. The holy grail of ion-neutral systems is reaching the quantum low-energy scattering regime, known as the s-wave scattering. However, in most atom-ion systems, there is a fundamental limit that prohibits reaching this regime. This limit arises from the time-dependent trapping potential of the ion, the Paul trap, which sets a lower collision energy limit which is higher than the s-wave energy. In this work, we studied both theoretically and experimentally, the way the Paul trap parameters affect the energy distribution of an ion that is immersed in a bath of ultra-cold atoms. Heating rates and energy distributions of the ion are calculated for various trap parameters by a molecular dynamics (MD) simulation that takes into account the attractive atom-ion potential. The deviation of the energy distribution from a thermal one is discussed. Using the MD simulation, the heating dynamics for different atom-ion combinations is also investigated. In addition, we performed measurements of the heating rates of a ground-state cooled 88 Sr + ion that is immersed in an ultra-cold cloud of 87 Rb atoms, over a wide range of trap parameters, and compare our results to the MD simulation. Both the simulation and the experiment reveal no significant change in the heating for different parameters of the trap. However, in the experiment a slightly higher global heating is observed, relative to the simulation.