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The Implementation of Slab Geometry for Membrane-Channel Molecular Dynamics Simulations

David Bostick ^* and Max L. Berkowitz 

^*Department of Physics and Program in Molecular/Cell Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599; and Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599

Correspondence: Address reprint requests to Max L. Berkowitz, Dept. of Chemistry, University of North Carolina, Chapel Hill, NC 27599. Tel.: 919-962-1218; Fax: 919-962-2388; E-mail: maxb{at}unc.edu.

Slab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties.

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