OpenMM 7.1.0 was used. The OpenMM simulations used the same systems loaded from the .prmtop and .inpcrd files as prepared in Section 2.3.1. For the MD portions of the protocol a Langevin integrator was used with a 2fs timestep and 1/ps collision rate. No barostat was used for these simulations after equilibration (and thus simulations were done in the NVT ensemble). Long range electrostatics were calculated using Particle Mesh Ewald.