Direct molecular simulation of gradient-driven diffusion

Thompson, Aidan P.; Ford, David M.; Heffelfinger, Grant S.

doi:10.1063/1.477284

Cited by 78 publications

(45 citation statements)

References 31 publications

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“…A color field acts as the driving force for diffusion, and the resulting flux is computed. A third technique, the dual control volume grand canonical molecular dynamics 265,266 (see section 2.5), involves two reservoirs in the zeolite that are maintained at different values of the chemical potential. This steady state nonequilibrium situation results in a flux that can be related directly to the transport diffusion coefficient.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity

2008

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Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity

2008

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“…9 GCMC/BD is closely related to the dual-volume-control molecular dynamics method ͑DVC/MD͒ which has been used to study diffusion problems through porous membranes. [21][22][23][24] The combined GCMC/BD algorithm with the present treatment of the reaction field using a generalized basis-set expansion provides a useful framework for simulating non-equilibrium ion fluxes through membrane channels.…”

Section: Introductionmentioning

confidence: 99%

Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

Im¹,

Roux²

2001

The Journal of Chemical Physics

105

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A general method has been developed to include the electrostatic reaction field in Brownian dynamics ͑BD͒ simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent is represented as a featureless continuum dielectric medium, a multipolar basis-set expansion is developed to express the reaction field Green's function. A reaction field matrix, which provides the coupling between generalized multipoles, is calculated only once and stored before the BD simulations. The electrostatic energy and forces are calculated at each time step by updating the generalized multipole moments. The method is closely related to the generalized solvent boundary potential ͓Im et al., J. Chem. Phys. 114, 2924 ͑2001͔͒ which was recently developed to include the influence of distant atoms on a small region part of a large macromolecular system in molecular dynamics simulations. It is shown that the basis-set expansion is accurate and computationally inexpensive for three simple models such as a spherical ionic system, an impermeable membrane system, and a cylindrical pore system as well as a realistic system such as OmpF porin with all atomic details. The influence of the static field and the reaction field on the ion distribution and conductance in the OmpF channel is studied and discussed.

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“…Recent efforts, however, have yielded grand canonical molecular dynamics (GCMD) methods (see [153] for a recent discussion of such methods). To date, however, only one GCMD simulation algorithm has been completely parallelized [154,155].…”

Section: Parallel Algorithms For Related Classical Simulation Methodsmentioning

confidence: 99%