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The successors of distributed-memory, massively-parallel processing (MPP) systems that are based on multi-core processor technologies and high-bandwidth communication networks are expected to deliver Petascale computing power for scientific communities in near future. This report presents preliminary performance evaluation and benchmarking results of a scalable biomolecular simulation framework on the Cray XT4 MPP system that contains multi-core Opteron processors. We identify not only the performance enhancing features but also the bottlenecks for biomolecular simulation test cases on this system using a combination of application and vendor specific performance tools. Our results show that unprecedented performance has been achieved for large-scale test cases on the system; however, the critical challenges remain for longer time scale simulations on MPP systems.