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. Author manuscript; available in PMC: 2017 Mar 1.
Published in final edited form as: Proteins. 2016 Feb 1;84(3):305–315. doi: 10.1002/prot.24969

Fig. 10.

Fig. 10

Left: Na+ (yellow spheres) surrounded by water inside the 7 pores that comprise the simulation system (pink transparent spheres represent the narrowest section of each pore). Force is applied only on Na+ ions. Each pore has a total charge of -1.2 e. Right: Different views of the same MD snapshot as in the Left snapshot. A) Na+ surrounded by water inside the pores. B) The same snapshot as A, except that the pore-lining atoms have been hidden to highlight the water structure inside the pore. There are 12-20 water molecules on average in the water cloud surrounding each ion. Note: In these images the water molecules are shown in bond representation and the carbon and sodium atoms as spheres with van der Waals radius for clarity. (If water molecules are depicted via van der Waals representation here, the figure becomes cluttered, leading to a loss of clarity concerning the essential molecular details of the process under study.)