We developed a computerised simulation that utilises embodied modelling by letting students play the role of particles in a liquid. We compared the learning of two eight-grade classrooms that used the embodied modelling simulation during a weeklong learning module on phase change, with a comparison group that used an ordinary simulation with no embodied modelling. In the pre-test, neither group mentioned inter-molecular forces in their explanations. In the post-test, significantly more students from the embodied modelling group mentioned inter-molecular bonds in their explanations than their counterparts who used the regular simulation, and realised that inter-molecular forces influence the motion of particles. However, we found little difference between the groups in students' ability to relate the magnitude of the inter-molecular forces to the magnitude of the boiling point of the material, showing not only the potential but also the limits in developing complex conceptualisations through this approach. Building on these findings, we discuss the affordances of embodied modelling for learning complex models, and suggest future directions for research into embodied modelling.