ing the PDB2PQR server. ParmEd () was used to convert the pqr output to a pdb file. For the ligands, OpenEye toolkits 56 were used to add missing hydrogen atoms and to check the bond order and connectivities. For toluene and the HSP90 ligand the binding mode was extracted from the crystal structure. An alternative binding mode of toluene and the binding mode of 3-iodotoluene were obtained from the supporting information of the BLUES paper. The systems of the protein-ligand complex and the ligand in solution were then generated using YANK. The protein was parameterized with Amberff14SB 59 and the ligands with GAFF2 60 and AM1-BCC charges. The protein-ligand complex was solvated with TIP3P water 62 in a cubic box and N a + and Cl -ions were added until a salt concentration of 50 mM (T4 lysozyme) or 150 mM (HSP90) was reached. The Amber output files of the system were then converted to GROMACS structure and topology files using ParmEd. For HSP90 two protein-ligand systems were prepared, one where all water molecules from the crystal structure were removed, while in the second crystallographic waters in the binding site were retained. The topology and coordinate files are available in the supporting information (SI).