Equinatoxin II (EqtII) is a 179-residue toxin from the venom of the sea anemone Actinia equina. EqtII is a member of the actinoporin family of proteins, which have potent lytic activity towards membranes containing sphingomyelin (SM). To gain insight into the atomic-level details governing SM selectivity, a series of all-atom molecular dynamics simulations were performed to model the binding of EqtII to micelles of n-dodecylphosphocholine (DPC) and acetyl-SM (Ac-SM). These models are in good agreement with our concurrent high-resolution solution NMR studies and prior data1 2 that suggest membrane binding is dependent on a conserved cluster of aromatic amino acids. Furthermore, methods have been developed to calculate the potential of mean force (PMF) over trajectories describing the approach and release of monomeric EqtII from DPC and Ac-SM micelles, which have provided valuable thermodynamic information regarding the attachment of EqtII to membranes, and possibly a mechanism responsible for SM selectivity.