In this Perspective, I review the current state of computational simulations on ionic liquids with an emphasis on the recent biocompatible variants. These materials are used here as an example of relatively complex systems that highlights the limits of some of the approaches commonly used to study their structure and dynamics. The source of these limits consists of the coexistence of nontrivial electrostatic, many-body quantum effects, strong hydrogen bonds, and chemical processes affecting the mutual protonation state of the constituent molecular ions. I also provide examples on how it is possible to overcome these problems using suitable simulation paradigms and recently improved techniques that, I expect, will be gradually introduced in the state-of-the-art of computational simulations of ionic liquids.