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. 2000 Aug;79(2):788–801. doi: 10.1016/S0006-3495(00)76336-3

A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels.

W Im 1, S Seefeld 1, B Roux 1
PMCID: PMC1300978  PMID: 10920012

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 (; 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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Selected References

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