We have developed an efficient computational scheme for integration of the classical Hamilton equations describing the ion dynamics confined in the radio-frequency field of the Paul trap. It has permitted a quantitative treatment of cold atom-ion resonant collisions in hybrid atom-ion traps with taking into account unremovable ion micromotion caused by the radio-frequency fields (V. S. https://poolsproductscanadas.shop/product-category/hydro-4-parts/