Simulations were performed at 298 K and all MD was performed using the Langevin BAOAB integrator with a friction coefficient of 1 ps -1 and a time step of 2 fs or, for MUP1, 4 fs with hydrogen mass partitioning (Hydrogen mass = 2 Da). Where appropriate, a Monte Carlo barostat is used to maintain a system pressure of 1 bar. The cut-off for nonbonded interactions was 12 Å with a switching function applied at 10 Å for the Lennard-Jones interactions. Particle mesh Ewald (PME) was used to calculate the effect of the long-range electrostatics. Owing to software limitations, the long-range dispersion correction is neglected, as per our previous work. The proteins T4L99A and MUP1 were modeled using the AMBER ff14SB forcefield . The Q4MD-CD forcefield, designed specifically for cyclodextrins, was used for the host βCD. All simulations use TIP3P waters and all ligands are parameterized using GAFF with AM1-BCC charges . Ions, wherever present, were modeled with Joung-Cheatham parameters.