It is now viable to use coarse-grained molecular dynamics (CGMD) to model interacting clay particles in simulations of soil mechanics element tests. In CGMD, particle interactions are described by the Gay-Berne (GB) potential, which can approximate the potential energy between clay particles as a function of their separation and relative orientations; however, a previous study identified a significant shortcoming of the GB potential, which is that it lacks a local maximum called the “energy barrier” that the true interaction possesses at very close range. In this study, we propose a modified GB potential which can capture the energy barrier at and we use this new potential function to simulate the clay mineral kaolinite under isotropic compression. Our simulations show that the energy barrier is a crucial ingredient required to reproduce the elastoplastic behaviour observed in laboratory tests upon unloading from an isotropic normally consolidated state. Our data show that the difference in mechanical behaviour between normally consolidated clay and overconsolidated clay can be explained by the fact that, during the initial loading, some pairs of interacting particles surmount the energy barrier so that they then experience a large attractive force. Effectively, these particles become bounded and do not separate when the stress applied to the sample is released. The response of overconsolidated clay to applied stress is stiffer than that of normally consolidated clay because a larger proportion of the clay particle interactions exist in this bonded state.