Molecular self-assembly is among the critical phenomena at the nanoscale as it provides the path of lowest energy consumption for the formation of nanostructures with controlled shapes and functions. Understanding factors that govern molecular recognition is therefore of fundamental interest and opens to the rational design of new materials. The ultimate goal of this UE is learning how to quantify molecular recognition (or binding) in solution by modeling and rigorous free-energy calculations based on Molecular Dynamics. The course is organized in the form of a tutored project carried out in groups that develops over six weeks. Every week, new theoretical/simulation material is presented and a demonstration on how to implement it is given in the computer room. In a second moment, the homework submitted by the students is analyzed and discussed live in a feedback session. At the end of the course, all groups present their results in front of the class and are graded by peers.