Skip to main content
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.
1.M. Karplus and J. A. McCammon, Nat. Struct. Biol. 9, 646 (2002);
1.C. L. Brooks and D. A. Case, Chem. Rev. (Washington, D.C.) 93, 2487 (1993);
1.D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed. (Academic, London, 2001);
1.W. Wang, O. Donini, C. M. Reyes, and P. A. Kollman, Annu. Rev. Biophys. Biomol. Struct. 30, 211 (2001);
1.T. Schlick, R. D. Skeel, A. T. Brunger, L. V. Kalé, J. A. Board, J. Hermans, and K. Schulten, J. Comput. Phys. 151, 9 (1999).
2.G. S. Almasi, C. Cascaval, J. G. Castanos et al., Int. J. Parallel Prog. 30, 317 (2002).
3.D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 26, 1701 (2005).
4.R. W. Hockney and J. W. Eastwood, Computer Simulation Using Particles (Adam Hilger, Bristol, 1988).
5.J. J. Monaghan, Annu. Rev. Astron. Astrophys. 30, 543 (1992).
6.G. S. Heffelfinger, Comput. Phys. Commun. 128, 219 (2000);
6.S. Plimpton, J. Comput. Phys. 117, 1 (1995).
7.K. J. Bowers, R. O. Dror, and D. E. Shaw, J. Phys.: Conf. Ser.16, 300 (2005).
8.K. J. Bowers, R. O. Dror, and D. E. Shaw, J. Comput. Phys. (in press).
9.D. E. Shaw, J. Comput. Chem. 26, 1318 (2005).
10.B. G. Fitch, A. Rayshubskiy, M. Eleftheriou et al., Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, IBM Report RC23688, IBM (2005).
11.B. G. Fitch, A. Rayshubskiy, M. Eleftheriou et al., Blue Matter: Strong Scaling of Molecular Dynamics on Blue Gene/L, IBM Report RC23888, IBM (2006).
12.One can only guarantee that an interaction between two particles residing in the same processor will be computed on that processor if the region assigned to that processor is convex.
13.We have discovered novel neutral territory methods whose import volume is slightly smaller than that of the midpoint and ES methods for small . These methods will be described in a subsequent paper.
14.M. Snir, Theory Comput. Syst. 37, 295 (2004).
15.These figures are approximate because we have ignored the constraints on box aspect ratios due to the finite number of processors. In order for the boxes to be exactly cubic when the global cell is cubic, for example, the number of processors must be the cube of some integer. In practice, one might choose not to use a few of the available processors in order to obtain more convenient aspect ratios.
16.Red Storm System Raises Bar on Supercomputer Scalability (Cray, Seattle, 2003);
16.N. R. Adiga, G. Almasi, G. S. Almasi et al., in Proceedings of the 3rd IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis, Jersey City, NJ, 207 (2005);
16.R. E. Kessler and J. L. Schwarzmeier, in 38th IEEE Comput. Soc. Intl. Conf., 176 (1993);
16.S. Scott and G. Thomas, in Proceedings of Hot Interconnects IV, 147 (1996).
17.J. MacKerell, D. Bashford, M. Bellott et al., J. Phys. Chem. B 102, 3586 (1998).
18.P. A. Kollman, R. W. Dixon, W. D. Cornell, T. Fox, C. Chipot, and A. Pohorille, in Computer Simulations of Biological Systems, edited by W. F. van Gunsteren (Kluwer, Dordrecht, Netherlands ESCOM, Leiden, 1997), Vol. 3, 83.
19.W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives, J. Am. Chem. Soc. 118, 11225 (1996).
20.W. R. P. Scott, P. H. Hünenberger, I. G. Tironi, A. E. Marks, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krüger, and W. F. van Gunsteren, J. Phys. Chem. A 103, 3596 (1999).
21.T. A. Halgren, J. Comput. Chem. 20, 730 (1999).<730::AID-JCC8>3.0.CO;2-T
22.C. L. Brooks, B. M. Pettit, and M. Karplus, J. Chem. Phys. 83, 5897 (1985);
22.P. Mark and L. Nilsson, J. Comput. Chem. 23, 1211 (2002);
22.J. Norberg and L. Nilsson, Biophys. J. 79, 1537 (2000);
22.M. Patra, M. Karttunen, T. Hyvönen, E. Falck, P. Lindqvist, and I. Vattulainen, Biophys. J. 84, 3636 (2003).
23.T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98, 10089 (1993);
23.U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen, J. Chem. Phys. 103, 8577 (1995).
24.C. Sagui and T. Darden, J. Chem. Phys. 114, 6578 (2001).
25.Y. Shan, J. L. Klepeis, M. P. Eastwood, R. O. Dror, and D. E. Shaw, J. Chem. Phys. 122, 054101 (2005).
26.J. Vidgren, L. A. Svensson, and A. Liljas, Nature (London) 368, 354 (1994).
27.H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, in Intermolecular Forces, edited by B. Pullman (Reidel, Dordrecht, 1981), 331.

Data & Media loading...


Article metrics loading...



The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.


Full text loading...


Access Key

  • FFree Content
  • OAOpen Access Content
  • SSubscribed Content
  • TFree Trial Content
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd