title: Reservoir boundaries in Brownian dynamics simulations of ion channels.
abstract: 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.
authors.affiliation: Department of Theoretical Physics, Research School of Physical Sciences, Australian National University, Canberra, Australian Capital Territory 0200, Australia.
authors.forename: Ben
authors.initials: B
authors.lastname: Corry
authors.forename: Matthew
authors.initials: M
authors.lastname: Hoyles
authors.forename: Toby W
authors.initials: TW
authors.lastname: Allen
authors.forename: Michael
authors.initials: M
authors.lastname: Walker
authors.forename: Serdar
authors.initials: S
authors.lastname: Kuyucak
authors.forename: Shin-Ho
authors.initials: SH
authors.lastname: Chung
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D002412:Cations; D002462:Cell Membrane / Q000378:metabolism; D003198:Computer Simulation; D004305:Dose-Response Relationship, Drug; D007477:Ions; D008564:Membrane Potentials; D015233:Models, Statistical; D009010:Monte Carlo Method; D015221:Potassium Channels; D013269:Stochastic Processes
chemical_list: D002412:Cations; D007477:Ions; D015221:Potassium Channels