The SEEKR2 calculations in this paper required both MD and BD simulations, which accept different sorts of inputs. The analysis (calculation of kinetics and thermodynamics quantities, error analysis, and convergence analysis) were performed by SEEKR2. When possible, temperatures, salt concentrations, and protonation states were set to recreate experimental conditions as closely as possible. One exception to this was the MD simulations of the βcyclodextrin "host" with the 1-or 2-naphylethanol "guest", which had 0.5M MnSO4 dissolved in solution for the experiment. Due to the inadequacy or lack of parameters for these divalent *13 ions, we elected to use pure water in these MD simulations, as we did with the other host-guest systems, which is consistent with previous studies. However, these salts were added to the BD simulations for the naphthylethanol molecules, since they were likely to significantly affect the rates of encounter. All ΔGbind values were computed using the formula ΔGbind = RT ln(koff / kon), where R is the gas constant, T is the temperature, and ln() is the natural logarithm function.