Cited references

1. W. F. van Gunsteren and H. J. C. Berendsen, “Computer Simulation of Molecular Dynamics: Methodology, Applications and Perspectives in Chemistry,” Angewandte Chemie International Edition in English 29, 992–1023 (1990).
2. A. R. C. Raine, D. Fincham, and W. Smith, “Sistolic Loop Methods for Molecular Simulation Using Multiple Transputers,” Computer Physics Communications 55, 13–30 (1989).
3. J. E. Mertz, D. J. Tobias, C. L. Brooks, and U. C. Singh, “Vector and Parallel Algorithms for the Molecular Dynamics Simulation of Macromolecules on Shared Memory Computers,” Journal of Computational Chemistry 12, 1270–1277 (1991).
4. S. L. Lin, J. Mellor-Crummey, B. M. Pettitt, and G. N. Phillips, “Molecular Dynamics on a Distributed Memory Multiprocessor,” Journal of Computational Chemistry 13, 1022–1035 (1992).
5. S. E. DeBolt and P. A. Kollman, “(AMBERCUBE) (MD), Parallelization of (AMBER)'s Molecular Dynamics Module for Distributed-Memory Hypercube Computers,” Journal of Computational Chemistry 14, 312–329 (1993).
6. Z. Fang, A. D. J. Haymet, W. Shinoda, and S. Okazaki, “Parallel Molecular Dynamics Simulation: Implementation of PVM for a Lipid Membrane,” Computer Physics Communications 116, No. 2–3, 295–310 (February 1999).
7. S. Plimpton and B. Hendrickson, “A New Parallel Method for Molecular Dynamics Simulation of Macromolecular Systems,” Journal of Computational Chemistry 17, 326–337 (February 1996).
8. S. Y. Liem, D. Brown, and J. H. R. Clarke, “Molecular Dynamics Simulations on Distributed Memory Machines,” Computer Physics Communications 67, 261–267 (1991).
9. D. Brown, J. H. R. Clarke, M. Okuda, and T. Yamazaki, “A Domain Decomposition Parallelization Strategy for Molecular Dynamics Simulations on Distributed Memory Machines,” Computer Physics Communications 74, 67–80 (1993).
10. T. W. Clark, R. v. Hanxleden, J. A. McCammon, and L. R. Scott, “Parallelizing Molecular Dynamics Using Spatial Decomposition,” Proceedings of the Scalable High Performance Computing Conference, Knoxville, TN (May 1994), pp. 95–102.
11. P. Ballestrero, P. Baglietto, and V. Ruggiero, “Molecular Dynamics for Proteins: Performance Evaluation on Massively Parallel Computers Based on Mesh Networks Using a Space Decomposition Approach,” Journal of Computational Chemistry 17, No. 4, 469–475 (1996).
12. T. P. Straatsma, “NWChem Molecular Dynamics Simulation,” Proceedings of High Performance Computing Systems and Applications (1998), pp. 231–239.
13. T. P. Straatsma, M. Philippopoulos, and J. A. McCammon, “NWChem: Exploiting Parallelism in Molecular Simulations,” Computer Physics Communications 128, No. 1–2, 377–385 (2000).
14. J. Anchell, E. Apra, D. Bernholdt, P. Borowski, T. W. Clark, D. Clerc, H. Dachsel, M. O. Deegan, M. Dupuis, K. Dyall, G. I. Fann, H. Fruchtl, M. Gutowski, R. J. Harrison, A. Hess, J. Jae, R. A. Kendall, R. Kobayashi, R. Kutteh, Z. Lin, R. Littlefield, X. Long, B. Meng, J. A. Nichols, J. Nieplocha, A. Rendall, M. Stave, T. P. Straatsma, H. Taylor, G. Thomas, K. Wolinski, and A. T. Wong, NWChem, A Computational Chemistry Package for Parallel Computers, Version 3.2.1, Pacific Northwest National Laboratory software computational chemistry applications classical molecular dynamics quantum mechanical calculations architecture memory domain decomposition intermolecular interactions periodic atomic reassignmentsoratory, Richland, WA 99352-0999 (1998). Further information on NWChem can be found under http://www.emsl.pnl.gov:2080/docs/nwchem.
15. R. A. Kendall, E. Apra, D. E. Bernholdt, E. J. Bylaska, M. Dupuis, G. I. Fann, R. J. Harrison, J. Ju, J. A. Nichols, J. Nieplocha, T. P. Straatsma, T. L. Windus, and A. T. Wong, “High Performance Computational Chemistry: An Overview of NWChem, a Distributed Parallel Application,” Computer Physics Communications 128, No. 1–2, 260–283 (2000).
16. J. Nieplocha, R. J. Harrison, and R. J. Littlefield, “Field Global Arrays: A Portable “Shared-Memory” Programming Model for Distributed Memory Computers,” Proceedings of Supercomputing '94 (1994), pp. 340–349. Further information on the global array library can be found under http://www.emsl.pnl.gov:2080/docs/parsoft.
17. G. N. Ramachandran and V. Sasisekharan, “Conformation of Polypeptides and Proteins,” Advances in Protein Chemistry 23, 283–437 (1968).
18. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, “Essential Dynamics of Proteins,” Proteins: Structure, Function, and Genetics 17, 412–425 (1993).
19. D. M. F. van Aalten, B. L. de Groot, J. B. C. Findlay, H. J. C. Berendsen, and A. Amadei, “A Comparison of Techniques for Calculating Protein Essential Dynamics,” Journal of Computational Chemistry 18, 169–181 (1997).
20. U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, T. H. Lee, and L. G. Pedersen, “A Smooth Particle Mesh Ewald Method,” Journal of Chemical Physics 103, No. 19, 8577–8593 (November 15, 1995).
21. L. V. Kale, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten, “NAMD2: Greater Scalability for Parallel Molecular Dynamics,” Journal of Computational Physics 151, No. 1, 283–312 (May 1, 1999).
22. L. Nyland, J. Prins, R. H. Yun, J. Hermans, H.-C. Kum, and L. Wang, “Achieving Scalable Parallel Molecular Dynamics Using Dynamic Spatial Domain Decomposition Techniques,” Journal of Parallel and Distributed Computing 47, No. 2, 125–138 (December 15, 1997).
23. G. Shah, J. Nieplocha, J. Mirza, C. Kim, R. Harrison, R. Govindaraju, K. Gildea, P. DiNicola, and C. Bender, “Performance and Experience with LAPI, a New High Performance Communication Library for the IBM RS/6000,” Proceedings of the First Merged International Parallel Processing Symposium and Symposium on Parallel and Distributed Processing, Orlando, FL (1998), pp. 260–266.