Reservoir Boundaries in Brownian Dynamics Simulations of Ion Channels

Ben Corry, M. Hoyles, T.W. Allen, M. Walker, S. Kuyucak, S. Chung

Research output: Contribution to journalArticle

57 Citations (Scopus)

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 BID 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.
Original languageEnglish
Pages (from-to)1975-1984
JournalBiophysical Journal
Volume82
Issue number4
DOIs
Publication statusPublished - 2002

Fingerprint Dive into the research topics of 'Reservoir Boundaries in Brownian Dynamics Simulations of Ion Channels'. Together they form a unique fingerprint.

Cite this