Weather models with high spatial and temporal resolutions are required for accurate prediction of meso-micro scale weather phenomena. Using these models for operational purposes requires forecasts with sufficient lead time, which in turn calls for large computational power. There exists a lot of prior studies on the performance of weather models on single domain simulations with a uniform horizontal resolution. However, there has not been much work on high resolution nested domains that are essential for high-fidelity weather forecasts. In this paper, we focus on improving and analyzing the performance of nested domain simulations using WRF on IBM Blue Gene/P. We demonstrate a significant reduction (up to 29%) in runtime via a combination of compiler optimizations, mapping of process topology to the physical torus topology, overlapping communication with computation, and parallel communications along torus dimensions. We also conduct a detailed performance evaluation using four nested domain configurations to assess the benefits of the different optimizations as well as the scalability of different WRF operations. Our analysis indicates that the choice of nesting configuration is critical for good performance. To aid WRF practitioners in making this choice, we describe a performance modeling approach that can predict the total simulation time in terms of the domain and processor configurations with a very high accuracy (< 8%) using a regression-based model learned from empirical timing data.