Multistate empirical valence bond simulations were employed to study proton transport through gramicidin A channels embedded in two different lipid bilayers, glycerol 1-monooleate (GMO) and diphytanolphosphatidylcholine (DiPhPC). Free energy barriers to proton permeation were derived using a new internal reaction coordinate describing the proton permeation process. The large quantitative and qualitative differences between the two systems are discussed in terms of local bilayer structures, ordering of interfacial water, and channel flexibility in the two environments.