SPEC CPU2000 Benchmark Description File Benchmark Name: 188.ammp Benchmark Author: Robert W. Harrison Benchmark Program General Category: Computational Chemistry. Modeling large systems of molecules usually associated with Biology. Benchmark Description: The benchmark runs molecular dynamics (i.e. solves the ODE defined by Newton's equations for the motions of the atoms in the system) on a protein-inhibitor complex which is embedded in water (see Harrison 1993 for descriptions of the algorithm and stability analysis on it). The energy is approximated by a classical potential or "force field". The protein is HIV protease complexed with the inhibitor indinavir. There are 9582 atoms in the water and protein making this representative of a typical large simulation. This benchmark is derived from published work on understanding drug resistance in HIV (Weber and Harrison 1999). Input Description: The problem tracks how the atoms move from an initial coorinates and initial velocities. Output Description: The output is the energy of the final configuration of atoms. Programming Language: C Known portability issues: none Reference: AMMP web site http://asterix.jci.tju.edu/ammp.html Harrison CV http://asterix.jci.tju.edu/harrisoncv.html Dynamics in AMMP Harrison R.W. (1993) Stiffness and energy conservation in molecular dynamics, an improved integrator J. Comp. Chem 14,1112-1122. Background on the benchmark Weber I.T. and Harrison R.W. (1999) Molecular mechanics analysis of drug resistant mutations of HIV protease Protein Engineering 12,469-474.