The modeling of ion-transport through biological membranes is important for understanding many life processes. The transmembrane potential and ion concentrations in the stationary state can be measured in in-vivo experiments. They can also be simulated within membrane models. Here we consider a basic model of ion transport that describes the time evolution of ion concentrations and potentials through a set of nonlinear ordinary differential equations. To reduce the computation time I have developed an application for simulation of the ion-flows through a membrane starting from an ensemble of initial conditions, optimized for a Graphical Processing Unit (GPU). The application has been designed for the CUDA (Compute Unified Device Architecture) technology. It is written in CUDA C programming language and runs on NVIDIA TESLA family of numerical accelerators. The calculation speed can be increased almost 1000 times compared with a sequential program running on the Central Processing Unit (CPU) of a typical PC.