We sought to compare force fields directly and therefore attempted to minimize additional differences among the simulations with each force field. In all simulations, we applied AM1-BCC partial atomic charges to both the host and guest molecules using the antechamber program in AmberTools16 . The host charges were calculated using a single glucose molecule with methoxy caps on the O1 and O4 alcohols (Figure ); each glucose monomer in the cyclodextrin polymer has identical charges. After removing the capping atoms, the net charge of the glucose monomer was -0.064 e. To ensure a neutrality of the glucose monomer, the charge remainder was proportionally distributed across all atoms according to the magnitude of the partial charge for each atom. The minimum and maximum charge adjustments were 0.000684 and 0.007245 e, respectively. Using the entire αCD molecule as an input to antechamber results in partial atomic charges that differ by at most 0.02 e, compared to using a single monomer, and requires reducing the maximum path length used to determine the equivalence of atomic charges (Figure ). We used TIP3P water and Joung-Cheatham monovalent ion parameters in each simulation set. GAFF v1.7 bond, angle, torsion, and Lennard-Jones parameters were applied using the tleap program distributed with AmberTools16. GAFF v2.1 parameters were applied in an identical manner to the GAFF v1.7 parameters, using the tleap program distributed with AmberTools18 and substituting leaprc.gaff for leaprc.gaff2 in the tleap input file.