The methodological features of using software systems for modeling the dynamics of mechanical systems for solving educational research problems are considered. The traditionally established approach to studying the foundations of modeling the dynamics of technical systems is largely based on mastering the corresponding mathematical tools. With regard to modeling the dynamics of systems of solids, the mentioned approach involves, first of all, the development of skills in the preparation of ordinary differential equations (ODEs). At the same time, the formation of a mechanical calculation scheme as an «object of application of mathematics» becomes a natural stage of mathematical research, and the selection of simplifying assumptions that allow one or another idealization to correspond to a real object is carried out consciously taking into account the desire for certain internal properties of the mathematical model (for example, type and order of the ODE system). An important feature of modern systems for modeling the dynamics of solid’s systems is the ability to describe the object under study directly in terms of the subject area. This feature provides an increase in the effectiveness of modeling in solving design and engineering and scientific research problems and allows you to save a qualified specialist from a laborious routine. At the same time, as experience shows, in the process of solving educational and research problems, due to the mentioned features of modern software, students have certain difficulties in mastering the fundamental conceptual base of the corresponding discipline (physics, electrical engineering, theoretical mechanics, theory of automatic control, fundamentals of computer aided design). The article gives an example of an educational research task focused on overcoming these difficulties.