Molecular dynamics is increasingly introduced in chemistry and life science courses, yet students often experience difficulties in interpreting simulation outputs and relating different descriptors to a coherent explanation. In this context, molecular dynamics can be approached as an interpretative practice rather than as a set of techniques. The experience described here was implemented in a graduate-level physical chemistry course for biotechnology students within a Team-Based Learning framework, designed to promote discussion, comparison of viewpoints and collective decision making based on available evidence. Particular attention is given to how students move from a descriptive reading of individual indicators to a more integrated interpretation through group interaction. The implementation and the observed learning dynamics are discussed, highlighting both strengths and critical aspects. The role of guided questioning, also supported by AI, is considered in relation to the development of students’ ability to construct and justify interpretations. The experience suggests that focusing on interpretation and decision making can contribute to making physical chemistry more meaningful and closer to scientific practice.