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A Grand Canonical Monte Carlo–Brownian Dynamics Algorithm for Simulating Ion Channels
Im, Wonpil Seefeld, Stefan Roux, Benoît
Im, Wonpil
Seefeld, Stefan
Roux, Benoît
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Abstract
A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formulation of the equilibrium properties of ion channels (Roux, B. 1999; Biophys. J. 77:139–153). The GCMC/BD algorithm is illustrated with simulations of simple test systems and of the OmpF porin of Escherichia coli. The approach provides a framework for simulating ion permeation in the context of detailed microscopic models.
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This is the published version. Copyright 2000 by Elsevier B. V.
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2000-08
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Elsevier B. V.
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wonpil-v79p788-801.pdf
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Im, Wonpil, Stefan Seefeld, and Benoît Roux. "A Grand Canonical Monte Carlo–Brownian Dynamics Algorithm for Simulating Ion Channels." Biophysical Journal 79.2 (2000): 788-801. http://dx.doi.org/10.1016/S0006-3495(00)76336-3.