352.nab
SPEC OMP2012 Benchmark Description

Benchmark Name

352.nab

Benchmark Author

Russ Brown et al

Benchmark Program General Category

Molecular Modeling

Benchmark Description

352.nab is based on Nucleic Acid Builder (NAB), which is a molecular modeling application that performs the types of floating point intensive calculations that occur commonly in life science computation. The calculations range from relatively unstructured "molecular dynamics" to relatively structured linear algebra.

Input Description

352.nab's input consists molecules with varying numbers of atoms.
Most of these inputs were culled from the Brookhaven Protein Data Bank at http://www.rcsb.org. They were processed into the format required by nab.

The input to the program is the directory to use and a random seed. The directory will contain the molecular topology (from .pdb file) and a molecular force field (from .prm file). The reference data set 1ea0 has 44794 atoms, the test data set hkrdenq has 124 atoms and the train data sets aminos has 327 atoms and gcn4 has 1957 atoms.

Output Description

The output is a report of the calculated energies at the various iterations counts.

Programming Language

ANSI C

Known portability issues

You need an OpenMP-compliant compiler and run-time libraries.

References

• The Case Group at Rutgers: http://www.casegroup.rutgers.edu
• The Brookhaven Protein Data Bank: http://www.rcsb.org
• T. Macke and D.A. Case. Modeling unusual nucleic acid structures. In Molecular Modeling of Nucleic Acids, N.B. Leontes and J. SantaLucia, Jr., eds. (Washington, DC: American Chemical Society, 1998), pp. 379-393. DOI

Last updated: $Date: 2012-06-29 14:01:56 -0400 (Fri, 29 Jun 2012) $