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Generalized Langevin models of molecular dynamics simulations with applications to ion channels

Gordon, Dan; Krishnamurthy, Vikram; Chung, Shin-Ho


We present a new methodology, which combines molecular dynamics and stochastic dynamics, for modeling the permeation of ions across biological ion channels. Using molecular dynamics, a free energy profile is determined for the ion(s) in the channel, and the distribution of random and frictional forces is measured over discrete segments of the ion channel. The parameters thus determined are used in stochastic dynamics simulations based on the nonlinear generalized Langevin equation. We first...[Show more]

CollectionsANU Research Publications
Date published: 2009-10-02
Type: Journal article
Source: The Journal of Chemical Physics
DOI: 10.1063/1.3233945


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