Allen, Toby; Bastug, Turgut; Kuyucak, Serdar; Chung, Shin-Ho
We use the well-known structural and functional properties of the gramicidin A channel to test the appropriateness of force fields commonly used in molecular dynamics (MD) simulations of ion channels. For this purpose, the high-resolution structure of the gramicidin A dimer is embedded in a dimyristoylphosphatidylcholine bilayer, and the potential of mean force of a K+ ion is calculated along the channel axis using the umbrella sampling method. Calculations are performed using two of the most...[Show more]
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