The free energies from each CV, along with the Boresch correction and the symmetry correction, are reported in Table , and representative PMFs are shown in Figures and for apCC-Di and CC-Di, respectively. The restrained metadynamics protocol correctly predicts the preferred topology for each dimer; CC-Di preferably forms a parallel dimer, and apCC-Di preferably forms an antiparallel dimer. Similar to the original geometrical route framework, the angle and dihedral PMFs contribute less than 1 kcal mol -1 each, which are small but not negligible contributions to the total binding free energy. The largest contribution is attributed to the separation PMF, as expected, reflecting the intermolecular interactions formed between 'receptor' and 'ligand' upon binding. Crucial differences between the parallel and antiparallel assemblies can already be observed from the separation PMF profiles (Figure ). Whilst the depth of the separation PMF does not correspond to the binding free energy due to the presence of restraints, it can be clearly seen that the parallel CC-Di and the antiparallel apCC-Di are the preferred structures. The separation PMFs have clear, distinct global minima (Figure ), with the exception of the parallel apCC-Di complex, which shows multiple minima in the 10-20 Å range. Isolation of the bound conformations from the separation PMF minima showed that reasonable structures were obtained. Analysis of inter-helical interactions showed that the contacts from the native coiled-coil structures were rescued (Figure ). Of notable importance are the Asn17-Asn17 hydrogen bond in CC-Di, and the Asp@e-Arg@a hydrogen bonds/salt bridges in apCC-Di, which determine the formation of parallel and antiparallel dimers, respectively. These interactions are observed in the restrained metadynamics simulations, whereas they are not as prominent in the unrestrained and funnel metadynamics simulations (Figures ). For comparison of dimers, it is not necessary to divide by the number of helices in the assembly, but this has been done here to facilitate comparisons with higher oligomerisation states.