Protegrins are small, cationic antimicrobial peptides (AMPs) that are believed to act against bacterial infections by compromising the integrity of the bacterial cell membrane. Experimental evidence suggests that protegrins, as well as other AMPs, act cooperatively to form nanoscale pore structures that completely disrupt normal membrane function. We have employed molecular dynamics simulations to study the structural features of an octameric protegrin pore in an anionic lipid bilayer. Structures obtained from the simulations are used as input to a continuum electrodiffusion analysis of ion permeation (commonly referred to as Poisson-Nernst-Planck theory). The coupled steady-state Poisson-Nernst-Planck equations are solved numerically, using the geometry, charge density, and ion diffusivity profile obtained from the MD simulations. This multiscale approach allows for a quantitative analysis of ion transport through a protegrin pore in the biologically relevant non-equilibrium state (in particular, ion transport in the presence of an applied field, or in the presence of a concentration gradient). The relatively low computational cost of this approach allows us to explore numerous aspects of ion transport through a protegrin pore, including current-voltage relationships, the relative importance of geometry and charge distribution, ion types and diffusivities, and external conditions. We have additionally extended this model to approximately capture the time-dependent ion concentration profiles through an entire cell, as well as the decay of the cellular transmembrane potential. In this approach, the cell membrane is modeled as a homogeneous layer with properties derived from the small-scale, single pore structure. The permeation of ions through the cell membrane and the resulting transmembrane potential loss are believed to be significant events in the bactericidal action of all antimicrobial peptides.