Desmond-Related Publications

An overview of the Desmond software can be found in the following paper, which won the "Best Paper Award" at the 2006 ACM/IEEE Conference on Supercomputing (SC06). If you'd like to cite Desmond in a publication, here's the reference that should be used:

• Kevin J. Bowers, Edmond Chow, Huafeng Xu, Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, and David E. Shaw, "Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters," Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17, 2006. Text

Further details about the performance of Desmond, the algorithms and implementation techniques used in Desmond, as well as application studies using Desmond, can be found in the following papers:

Performance

• Edmond Chow, Charles A. Rendleman, Kevin J. Bowers, Ron O. Dror, Douglas H. Hughes, Justin Gullingsrud, Federico D. Sacerdoti, and David E. Shaw, "Desmond Performance on a Cluster of Multicore Processors," D. E. Shaw Research Technical Report DESRES/TR--2008-01, July 2008. Text

Parallelization methods

• David E. Shaw, "A Fast, Scalable Method for the Parallel Evaluation of Distance-Limited Pairwise Particle Interactions," Journal of Computational Chemistry, vol. 26, no. 13, 2005, pp. 1318–1328. Text
• Kevin J. Bowers, Ron O. Dror, and David E. Shaw, "The Midpoint Method for Parallelization of Particle Simulations," Journal of Chemical Physics, vol. 124, no. 18, 2006, pp. 184109:1–11. Text
• Kevin J. Bowers, Ron O. Dror, and David E. Shaw, "Zonal Methods for the Parallel Execution of Range-Limited N-Body Simulations," Journal of Computational Physics, vol. 221, no. 1, 2007, pp. 303–329. Text

Numerical methods

• Ross A. Lippert, Kevin J. Bowers, Ron O. Dror, Michael Eastwood, Brent A. Gregersen, John L. Klepeis, István Kolossváry, and David E. Shaw, "A Common, Avoidable Source of Error in Molecular Dynamics Integrators," Journal of Chemical Physics, vol. 126, no. 4, 2007, pp. 046101:1–2. Text

Long-range electrostatics

• Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror and David E. Shaw, "Gaussian Split Ewald: A Fast Ewald Mesh Method for Molecular Simulation," Journal of Chemical Physics, vol. 122, no. 5, 2005, pp. 054101:1–13. Text

Applications using Desmond

• Isaiah T. Arkin, Huafeng Xu, Morten Ø. Jensen, Eyal Arbely, Estelle R. Bennett, Kevin J. Bowers, Edmond Chow, Ron O. Dror, Michael P. Eastwood, Ravenna Flitman-Tene, Brent A. Gregersen, John L. Klepeis, István Kolossváry, Yibing Shan, and David. E. Shaw, "Mechanism of Na⁺/H⁺ Antiporting," Science, vol. 317, no. 5839, 2007, pp. 799–803. Text
• Paul Maragakis, Kresten Lindorff-Larsen, Michael P. Eastwood, Ron O. Dror, John L. Klepeis, Isaiah T. Arkin, Morten Ø. Jensen, Huafeng Xu, Nikola Trbovic, Richard A. Friesner, Arthur G. Palmer III, and David E. Shaw, "Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins," Journal of Physical Chemistry B, vol. 112, no. 19, 2008, pp. 6155–6158. Text
• Morten Ø. Jensen, Ron O. Dror, Huafeng Xu, David W. Borhani, Isaiah T. Arkin, Michael P. Eastwood, and David E. Shaw, "Dynamic Control of Slow Water Transport by Aquaporin 0: Implications for Hydration and Junction Stability in the Eye Lens," Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 36, 2008, pp. 14430–14435. Text