Performance characterization of molecular dynamics techniques for biomolecular simulations

Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, PPOPP

Volumn 2006, Issue , 2006, Pages 59-68

  Alam, Sadaf R ^a   Vetter, Jeffrey S ^a   Agarwal, Pratul K ^a   Geist, Al ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Computational biology; Molecular dynamics algorithms; Performance analysis; Workload characterization

Indexed keywords

ALGORITHMS; COMPUTER SIMULATION; MOLECULAR BIOLOGY; PARALLEL PROCESSING SYSTEMS; PROBLEM SOLVING; PROGRAM PROCESSORS; SUPERCOMPUTERS;

COMPUTATIONAL BIOLOGY; COMPUTING POWER; PARTICLE MESH EWALD (PME); PERFORMANCE ANALYSIS; WORKLOAD CHARACTERIZATION;

MOLECULAR DYNAMICS;

EID: 33751040386     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1122971.1122983     Document Type: Conference Paper

References (23)

1. mpiP: Lightweight, Scalable MPI Profiling. http://www.llnl.gav/CASC/mpip/ .
2. P. K. Agarwal. Enzymes: An integrated view of structure, dynamics and function. Microbial Cell Factories, 5:2, 2006.
3. P. K. Agarwal. Role of Protein Dynamics in Reaction Rate Enhancement by Enzymes. Journal of American Chemical Society, 2005.
4. P. K. Agarwal, A. Geist, and A. Gorin. Protein Dynamics and Enzymatic Catalysis: Investigating the Peptidyl-Prolyl cis/trans Isomerization Activity of Cyclophilin A. Biochemistry, 43, 2004.
5. G. S. Almasi, C. Cascaval, J. G. Castanos, M. Denneau, W. E. Donath, M. Eleftheriou, M. Giampapa amd H. Ho, D. Lieber, J. E. Moreira, D. M. Newns, M. Snir, and H. S. Warren Jr. Demonstrating the Scalability of a Molecular Dynamics Application on a Petaflops Computer. International Journal of Parallel Programming, 30(4), 2002.
6. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4, 1983.
7. S. Browne, J. Dongarra, N. Gamer, G. Ho, and P. Mucci. A portable programming interface for performance evaluation on modern processors. The International Journal of High Performance Computing Applications, 2000.
8. T. Darden, D. York, and L. Pederson. Particle mesh Ewald-an Nlog(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98, 1993.
9. B. G. Fitch, R. S. Germain, M. P. Mendell, J. Pitera, M. Pitman, A. Rayshubskiy, Y. Y. Sham, F. Suits, W. C. Swope, T. J. C. Ward, Y. Zhestkov, and R. Zhou. Blue Matter, an application framework for molecular simulation on Blue Gene. Journal of Parallel and Distributed Computing, 63, 2003.
10. N. Goodman. Biological data becomes computer literate: new advances in bioinformatics. Curr. Opin. Biotechnol., 13(1), 2002.
11. GROMACS. http://www.gromacs.org/.
12. K. Hiroaki. Computational systems biology. Nature, 420, 2002.
13. L. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and title = "NAMD2 : Greater scalability for parallel molecular dynamics K. Schulten". NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151, 1999.
14. M. Karplus and G.A. Petsko. Molecular dynamics simulations in biology. Nature, 347, 1990.
15. A. R. Leach. Molecular Modelling: Principles and Applications. Prentice Hall, 2001.
16. D. A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, III T.E. Cheatham, S. DeBolt, D. Ferguson, G. Seibel, and P.Kollman. AMBER, a package of computer programs for applying molecular mechanics, normalmode analysis, molecular dynamics and free energy calculationsto simulate the structural and energetic properties of molecules. Computer Physics Communication, 91, 1995.
17. J. C. Phillips, G. Zheng, and L. Kale. NAMD: Biomolecular simulation on thousands of processors. In Supercomputing, 2002.
18. S. J. Plimpton. Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117, 1995.
19. IBM Blue Gene team. Blue Gene: A vision for protein science using a petaflop supercomputer. IBM Systems Jornal, 40, 2001.
20. IBM Blue Gene/L Team. An Overview of the Blue Gene/L supercomputer. In Supercomputing 2002.
21. V. Tsui and D.A. Case. Theory and applications of the generalized born solvation model in macromolecular simulations. Biopolymers (Nucl. Acid. Sci.), 56, 2001.
22. J. Vetter, S. Alam, T. Dunigan, M. Fahey, P. Roth, and P. Worley. Early evaluation of the Cray XT3. In 20th IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2006.
23. G. Zheng, T. Wilmarth, P. Jagadishprasad, and L. V. Kale. Simulation-based Performance Prediction for Large Parallel Machines. International Journal of Parallel Programming, 33(2-3), 2005.