ArticleBiophysical chemistry2006
Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods.
Article in Biophysical chemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Permeability Benchmarking: Guidelines for ComparingJournal of chemical information and modeling · 2025Review
- Molecular Dynamics Simulations of Membrane Permeability.Chemical reviews · 2019Review
- Subdiffusion in Membrane Permeation of Small Molecules.Scientific reports · 2016Article
- Two Relations to Estimate Membrane Permeability Using Milestoning.The journal of physical chemistry. B · 2016Article
- Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.Journal of chemical information and modeling · 2016Article
- The adaptive biasing force method: everything you always wanted to know but were afraid to ask.The journal of physical chemistry. B · 2015Article
- Arrayed lipid bilayer chambers allow single-molecule analysis of membrane transporter activity.Nature communications · 2014Article
- Multiscale Multiphysics and Multidomain Models I: Basic Theory.Journal of theoretical & computational chemistry · 2013Article
- Hydrogel-stabilized droplet bilayers for high speed solution exchange.Scientific reports · 2013Article
- Interacting ions in biophysics: real is not ideal.Biophysical journal · 2013Review
- Atomic-level simulation of current-voltage relationships in single-file ion channels.The Journal of general physiology · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics.The journal of physical chemistry. C, Nanomaterials and interfaces · 2012Article
- Variational multiscale models for charge transport.SIAM review. Society for Industrial and Applied Mathematics · 2012Article
- Testing the applicability of Nernst-Planck theory in ion channels: comparisons with Brownian dynamics simulations.PloS one · 2011Article
- Soft wall ion channel in continuum representation with application to modeling ion currents in α-hemolysin.The journal of physical chemistry. B · 2010Article
- Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel.Journal of the American Chemical Society · 2010Article
- Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids.The Journal of chemical physics · 2010Article
- Simulation of nanoparticle permeation through a lipid membrane.Biophysical journal · 2010Article
- Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport.Biochimica et biophysica acta · 2009Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The local diffusion constant of K(+) inside the Gramicidin A (GA) channel has been calculated using four computational methods based on molecular dynamics (MD) simulations, specifically: Mean Square Displacement (MSD), Velocity Autocorrelation Function (VACF), Second Fluctuation Dissipation Theorem (SFDT) and analysis of the Generalized Langevin Equation for a Harmonic Oscillator (GLE-HO). All methods were first tested and compared for K(+) in bulk water--all predicted the correct diffusion constant. Inside GA, MSD and VACF methods were found to be unreliable because they are biased by the systematic force exerted by the membrane-channel system on the ion. SFDT and GLE-HO techniques properly unbias the influence of the systematic force on the diffusion properties and predicted a similar diffusion constant of K(+) inside GA, namely, ca. 10 times smaller than in the bulk. It was found that both SFDT and GLE-HO methods require extensive MD sampling on the order of tens of nanoseconds to predict a reliable diffusion constant of K(+) inside GA.
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