We then employed our protocol to assess whether we can predict the preferred topology of a higher order coiled coil, separating one helix from the assembly at a time. To this end, the coiled-coil trimer CC-Tri was simulated as an all-parallel trimer (native structure) and as an up-down-up variant (competing structure). Interestingly, the parallel CC-Tri was the only higher order assembly whose 'receptor' (helices B-C) could re-organise from a 'closed' to an 'open' conformation during the trimer separation simulations, and did not necessitate the use of RMSD restraints on the receptor helices, although this did not happen reproducibly.