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SPEC CPU2000 Benchmark Description File

Benchmark Name


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


Known portability issues



AMMP web site

Harrison CV

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.

Last Updated: 14 October 1999