ArticleBiophysical journal2003
The implementation of slab geometry for membrane-channel molecular dynamics simulations.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- The role of structural order in heterogeneous ice nucleation.Chemical science · 2022Article
- The atomistic details of the ice recrystallisation inhibition activity of PVA.Nature communications · 2021Article
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- Multi-Level Ewald: A hybrid multigrid / Fast Fourier Transform approach to the electrostatic particle-mesh problem.Journal of chemical theory and computation · 2010Article
- A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1).PLoS computational biology · 2009Article
- Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study.Biophysical journal · 2008Article
- Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel.PLoS computational biology · 2007Article
- Voltage-dependent hydration and conduction properties of the hydrophobic pore of the mechanosensitive channel of small conductance.Biophysical journal · 2006Article
- Lipid-protein interactions of integral membrane proteins: a comparative simulation study.Biophysical journal · 2004Article
- OmpT: molecular dynamics simulations of an outer membrane enzyme.Biophysical journal · 2004Article
- Exterior site occupancy infers chloride-induced proton gating in a prokaryotic homolog of the ClC chloride channel.Biophysical journal · 2004Article
- Filter flexibility and distortion in a bacterial inward rectifier K+ channel: simulation studies of KirBac1.1.Biophysical journal · 2004Article
- Ionic permeation free energy in gramicidin: a semimicroscopic perspective.Biophysical journal · 2004Article
- KcsA closed and open: modelling and simulation studies.European biophysics journal : EBJ · 2004Article
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2 authors.
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Abstract
Slab geometric boundary conditions are applied in the molecular dynamics simulation of a simple membrane-channel system. The results of the simulation were compared to those of an analogous system using normal three-dimensional periodic boundary conditions. Analysis of the dynamics and electrostatics of the system show that slab geometric periodicity eliminates the artificial bulk water orientational polarization that is present while using normal three-dimensional periodicity. Furthermore, even though the water occupancy and volume of our simple channel is the same when using either method, the electrostatic properties are considerably different when using slab geometry. In particular, the orientational polarization of water is seen to be different in the interior of the channel. This gives rise to a markedly different electric field within the channel. We discuss the implications of slab geometry for the future simulation of this type of system and for the study of channel transport properties.
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