Fig. 2. Potentials of mean force along the center-of-mass distance between Y99 in the binding groove and P2 and E2 at the peptide N-terminus for (a) HLA-B*35:01 and (b) HLA-B*44:02, respectively. In (a), the PMF that was obtained with AMBER99SB*-ILDNP as protein force field and TIP4P/2005 as water model and published previously (blue line)²⁸ is included to facilitate comparisons with the PMFs obtained in this study (black and red line). The BEUS simulation yielding the PMF shown in red was started from the final configurations of the BEUS simulation with AMBER99SB*-ILDNP and TIP4P/2005.