A wide range of functions, such as proton transport and cell signaling, illustrate the importance of transmembrane proteins in biological phenomena. Elucidating the chemical and biochemical behavior of these proteins is the subject of much research. To this end, many experimental techniques have been employed to study membrane-protein systems, including spectroscopic and calorimetric methods. Computational methods including implicit membrane models, coarse-grained, and all-atom molecular dynamics (MD) simulations6 have complemented the experimental work. The all-atom method treats nearly every atom of the system in an explicit fashion, meaning that each atom is parameterized and simulated according to the MD equations. Standard software packages can execute these all-atom MD simulations.

Many large transmembrane protein receptors play vital roles in clinical applications. For instance, the nicotinic acetylcholine receptor (nAChR) can serve as a useful target in the efforts of smoking cessation, counter drug addiction and pain management. Yet, there are no highresolution structures of nAChR, thus making it a difficult pharmacological target. There exist several resolved structures of the acetylcholine binding protein (AChBP), which is an aqueous protein that mimics the binding and activity of the extra-cellular domain in nAChR. Thus, we intend to use AChBP as the target, to identify new small-molecule ligands that could become potential pharmaceuticals against nAChR. Such ligands may also help distinguish between the chemical features of AChBP and the various subtypes of nAChR.