At the same time, software and hardware development enable experts in the field to push the limits of MD simulations towards increasingly complex and large systems, such as cell membrane mimics and virus particles. In both of these lines of development, it is increasingly important to understand the consequences arising from the approximations in the classical potential functions, i.e., force field, and simulation algorithms used in MD simulations. The new wave of users, consisting of practitioners with varying experience on methodological details, are often unaware of these limitations. At the same time, increasing the size, time scale, and complexity of the simulated systems may lead to the multiplication or cancellation of errors in the physical description of the systems. Furthermore, with the growing impact of MD simulations in biomedical and other applications, the potentially incorrect or misleading results will have increasingly severe consequences. Therefore, improving the MD methodology and the protocols to evaluate the quality of MD simulations is becoming more and more important.