188.ammp
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
Harrison CV
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Dynamics in AMMP
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Harrison R.W. (1993) Stiffness and energy conservation in molecular
dynamics, an improved integrator J. Comp. Chem 14,1112-1122.
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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
