Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scal-able program. It is also… (More)
Parallel languages are tools for constructing eecient application programs, while reducing the required labor. In this light, using the most appropriate tool for each component of a complex system seems natural, resulting in multi-paradigm multilingual programming. The Converse system developed at Illinois addresses the issues involved in supporting… (More)
Parallel molecular dynamics programs employing shared memory or replicated data architectures encounter problems scaling to large numbers of processors. Spatial decomposition schemes offer better performance in theory, but often suffer from complexity of implementation and difficulty in load balancing. In the program NAMD 2, we have addressed these issues… (More)
Understanding interactions among various components in a distributed system is very important for system administrators and application developers. The System Monitoring Tool 1 (SMT) was developed to help in this regard for the OSF/DCE environment. SMT consists of two components: a remote monitoring agent to capture packets, and a management workstation… (More)
method for Ewald sums in large systems. Absolute comparison of simulated and experimental protein-folding dynamics.