Constant electric field simulations of the membrane potential illustrated with simple systems

Abstract

Advances in modern computational methods and technology make it possible to carry out extensive molecular dynamics simulations of complex membrane proteins based on detailed atomic models. The ultimate goal of such detailed simulations is to produce trajectories in which the behavior of the system is as realistic as possible. A critical aspect that requires consideration in the case of biological membrane systems is the existence of a net electric potential difference across the membrane. For meaningful computations, it is important to have well validated methodologies for incorporating the latter in molecular dynamics simulations. A widely used treatment of the membrane potential in molecular dynamics consists of applying an external uniform electric field E perpendicular to the membrane. The field acts on all charged particles throughout the simulated system, and the resulting applied membrane potential V is equal to the applied electric field times the length of the periodic cell in the direction perpendicular to the membrane. A series of test simulations based on simple membrane-slab models are carried out to clarify the consequences of the applied field. These illustrative tests demonstrate that the constant-field method is a simple and valid approach for accounting for the membrane potential in molecular dynamics studies of biomolecular systems.

Maxwell-Hall access resistance in graphene nanopores

“…We note that some previous studies have shown the dependence of the ionic current on the cell height [60,61]. However, in Ref.…”

“…The fit accurately determines R∞. Hence, the small simulation sizes in all-atom MD should be sufficient to obtain R∞.We note that some previous studies have shown the dependence of the ionic current on the cell height [60,61]. However, in Ref.…”

“…However, in Ref. 60, the dependence is examined in the context of changing field with the height and, in Ref. 61, the difference is considered insignificant.…”

Exploring the Membrane Potential of Simple Dual-Membrane Systems as Models for Gap-Junction Channels

“…Notwithstanding the fact that all-atom simulation approaches of similar macromolecular assemblies have been carried out (20,21), the understanding of the underlying mechanisms governing the behavior of these complex and large structures requires the development of simpler (and less computational demanding) model systems to evaluate working hypotheses. Following this approach, previous studies have shown that the basic features of voltage effects are preserved when employing simple pore models in molecular dynamics (MD) simulations, permitting an atomistic description of transport and structural properties, resulting voltages and thermodynamics (4,(22)(23)(24)(25).…”

Tension moderation and fluctuation spectrum in simulated lipid membranes under an applied electric potential

“…Subsequently we applied transmembrane potentials of 200 mV and 500 mV. We did so by applying a uniform external electric field E ext along the z axis in the simulation box such that V = E ext L z where V is the applied electric potential and L z the average box height [25], giving an applied electric field no greater than E ext ≈ 27.5 mV/nm. All simulations were performed using GROMACS 4.5.5 [26][27][28].…”