We examine the validity of the harmonic approximation, where the radio-frequency ion trap is treated as a harmonic trap, in the problem regarding the controlled collision of a trapped atom and a single trapped ion. This is equivalent to studying the effect of the micromotion since this motion must be neglected for the trapped ion to be considered as a harmonic oscillator. By applying the transformation of Cook and Shankland we find that the micromotion can be represented by two periodically oscillating operators. In order to investigate the effect of the micromotion on the dynamics of a trapped atom-ion system, we calculate (i) the coupling strengths of the micromotion operators by numerical integration and (ii) the quasienergies of the system by applying the Floquet formalism, a useful framework for studying periodic systems. It turns out that the micromotion is not negligible when the distance between the atom and the ion traps is shorter than a characteristic distance. Within this range the energy diagram of the system changes remarkably when the micromotion is taken into account, which leads to undesirable consequences for applications that are based on an adiabatic process of the trapped atom-ion system. We suggest a simple scheme for bypassing the micromotion effect in order to successfully implement a quantum controlled phase gate proposed previously and create an atom-ion macromolecule. The methods presented here are not restricted to trapped atom-ion systems and can be readily applied to studying the micromotion effect in any system involving a single trapped ion.Comment: 25 pages, 8 figure

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