The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters
Abstract
Although molecular dynamics (MD) simulations of biomolecular systems often run for days to months, many events of great scientific interest and pharmaceutical relevance occur on long time scales that remain beyond reach. We present several new algorithms and implementation techniques that significantly accelerate parallel MD simulations compared with current state-of-the-art codes. These include a novel parallel decomposition method and message-passing techniques that reduce communication requirements, as well as novel communication primitives that further reduce communication time. We have also developed numerical techniques that maintain high accuracy while using single precision computation in order to exploit processor-level vector instructions. These methods are embodied in a newly developed MD code called Desmond that achieves unprecedented simulation throughput and parallel scalability on commodity clusters. Our results suggest that Desmond's parallel performance substantially surpasses that of any previously described code. For example, on a standard benchmark, Desmond's performance on a conventional Opteron cluster with 2K processors slightly exceeded the reported performance of IBM's Blue Gene/L machine with 32K processors running its Blue Matter MD code.
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Cites
Fast Parallel Algorithms for Short-Range Molecular Dynamics
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Scalable molecular dynamics with NAMD
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The Amber biomolecular simulation programs
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Cited by
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005659 · Cited by 2,748
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
McGibbon, R. T., Beauchamp, K. A., Harrigan, M. P., Klein, C., Swails, J. M., Hernández, C. X., Schwantes, C. R., Wang, L.-P., Lane, T. J., & Pande, V. S. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.08.015 · Cited by 2,373
How fast-folding proteins fold
Lindorff-Larsen, K., Piana, S., Dror, R. O., & Shaw, D. E. (2011) · Science · doi:10.1126/science.1208351 · Cited by 1,980
Self-citationWang, L., Wu, Y., Deng, Y., Kim, B., Pierce, L., Krilov, G., Lupyan, D., Robinson, S., Dahlgren, M. K., Greenwood, J., et al. (2015) · Journal of the American Chemical Society · doi:10.1021/ja512751q · Cited by 1,313
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
Salo-Ahen, O. M. H., Alanko, I., Bhadane, R., Bonvin, A. M. J. J., Honorato, R. V., Hossain, S., Juffer, A. H., Kabedev, A., Lahtela-Kakkonen, M., Larsen, A. S., et al. (2020) · Processes · doi:10.3390/pr9010071 · Cited by 659
Metadata
- Authors
- Bowers, K. J., Sacerdoti, F. D., Salmon, J. K., Shan, Y., Shaw, D. E., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., & Moraes, M. A.
- Venue
- Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06
- Publisher
- ACM Press
- Published
- 2006
- Pages
- 84
- OpenAlex
- W2153228625
- Cited by
- 2,580
- References
- 3
- Type
- conference abstract
- Language
- en
- Open access
- closed
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- Bowers, K. J., Sacerdoti, F. D., Salmon, J. K., Shan, Y., Shaw, D. E., Chow, E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., & Moraes, M. A. (2006). Molecular dynamics---Scalable algorithms for molecular dynamics simulations on commodity clusters. Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06. https://doi.org/10.1145/1188455.1188544
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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