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Molecular Physics
An International Journal at the Interface Between Chemistry and Physics
Volume 100, 2002 - Issue 18
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Original Articles

Permeation of ions through a model biological channel: effect of periodic boundary conditions and cell size

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Pages 3011-3019 | Received 08 Aug 2001, Accepted 11 Jan 2002, Published online: 16 Nov 2009
 

Abstract

The effect of the simulation cell size and periodic boundary conditions on non-equilibrium molecular dynamics simulations of the structure and dynamics with explicit water molecules and ions in and near a model channel in a biological membrane is considered. The approach seems satisfactory. In particular, the presence of image channels that often contain image ions seems to have little effect on the average structure, channel content, or current for this system.

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