This research leads to a PC-based molecular mechanics software package that executes the most compute-intensive simulation and minimization functions in parallel on the APx massively-parallel processor. It will be possible to link this software package with a PC version of the AMBER molecular mechanics and dynamics software system, replacing the corresponding AMBER subroutines. The result will be a tool with the conformational analysis capabilities of AMBER, a cost within the capital budget of an individual researcher, local, desktop computing, avoiding the delays of remote jobs, and performance approaching that of Convex and Cray systems - approaching interactive response times, even for large simulations. In the future, this software package can be adapted to link with other molecular mechanics and graphics display programs. Phase 1 results will be a baseline version of AMBER that executes on a 386 or 486 PC, a PC version of AMBER that contains at least one APx-accelerated function, a report summarizing the PC/APx-related design issues, their solution and a development plan for Phase 2.
