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Biophys J, April 2002, p. 1975-1984, Vol. 82, No. 4

Reservoir Boundaries in Brownian Dynamics Simulations of Ion Channels

Ben Corry,dagger Matthew Hoyles,* Toby W. Allen,* Michael Walker,* Serdar Kuyucak,dagger and Shin-Ho Chung*

 *Protein Dynamics Unit, Department of Physics, Faculty of Science, and  dagger Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, Australian Capital Territory 0200, Australia

Brownian dynamics (BD) simulations provide a practical method for the calculation of ion channel conductance from a given structure. There has been much debate about the implementation of reservoir boundaries in BD simulations in recent years, with claims that the use of improper boundaries could have large effects on the calculated conductance values. Here we compare the simple stochastic boundary that we have been using in our BD simulations with the recently proposed grand canonical Monte Carlo method. We also compare different methods of creating transmembrane potentials. Our results confirm that the treatment of the reservoir boundaries is mostly irrelevant to the conductance properties of an ion channel as long as the reservoirs are large enough.

Biophys J, April 2002, p. 1975-1984, Vol. 82, No. 4
© 2002 by the Biophysical Society   0006-3495/02/04/1975/10  $2.00


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