The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
Abstract
The smooth particle mesh Ewald summation method is widely used to efficiently compute long-range electrostatic force terms in molecular dynamics simulations, and there has been considerable work in developing optimized implementations for a variety of parallel computer architectures. We describe an implementation for Nvidia graphical processing units (GPUs) which are general purpose computing devices with a high degree of intrinsic parallelism and arithmetic performance. We find that, for typical biomolecular simulations (e.g., DHFR, 26K atoms), a single GPU equipped workstation is able to provide sufficient performance to permit simulation rates of ≈50 ns/day when used in conjunction with the ACEMD molecular dynamics package (1) and exhibits an accuracy comparable to that of a reference double-precision CPU implementation.
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Cites
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
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Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.11.002 · Cited by 409
Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver
Miao, L., Lin, J., Huang, Y., Li, L., Delcassian, D., Ge, Y., Shi, Y., & Anderson, D. G. (2020) · Nature Communications · doi:10.1038/s41467-020-16248-y · Cited by 343
Rocklin, G. J., Mobley, D. L., Dill, K. A., & Hünenberger, P. H. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4826261 · Cited by 234
EMMA: A Software Package for Markov Model Building and Analysis
Senne, M., Trendelkamp-Schroer, B., Mey, A. S. J. S., Schütte, C., & Noé, F. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct300274u · Cited by 148
Kinetic characterization of the critical step in HIV-1 protease maturation
Sadiq, S. K., Noé, F., & De Fabritiis, G. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210983109 · Cited by 102
Self-citationMertmann, P., Eremin, D., Mussenbrock, T., Brinkmann, R. P., & Awakowicz, P. (2011) · Computer Physics Communications · doi:10.1016/j.cpc.2011.05.012 · Cited by 39
Lone, S. A., Khan, S., & Ahmad, A. (2020) · Archives of Microbiology · doi:10.1007/s00203-019-01781-2 · Cited by 32
Nemergut, M., Marques, S. M., Uhrik, L., Vanova, T., Nezvedova, M., Gadara, D. C., Jha, D., Tulis, J., Novakova, V., Planas-Iglesias, J., et al. (2023) · Molecular Neurodegeneration · doi:10.1186/s13024-023-00620-9 · Cited by 30
Tyrosine oxidation and nitration in transmembrane peptides is connected to lipid peroxidation
Bartesaghi, S., Herrera, D., Martinez, D. M., Petruk, A., Demicheli, V., Trujillo, M., Martí, M. A., Estrín, D. A., & Radi, R. (2017) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2017.04.006 · Cited by 18
Cui, S., Dasgupta, S., Yagi, S., Kimura, M., Furukawa, R., Tagami, S., & Akanuma, S. (2025) · Protein Science · doi:10.1002/pro.70071 · Cited by 12
Sadiq, S. K., Muñiz Chicharro, A., Friedrich, P., & Wade, R. C. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00673 · Cited by 8
Giorgino, T., Harvey, M. J., & de Fabritiis, G. (2010) · Computer Physics Communications · doi:10.1016/j.cpc.2010.04.007 · Cited by 8
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Metadata
- Authors
- Harvey, M. J., & De Fabritiis, G.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-08-14
- Volume
- 5
- Issue
- 9
- Pages
- 2371-2377
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W1994778680
- Cited by
- 408
- References
- 1
- FWCI
- 24.54
- Type
- journal article
- Language
- en
- Open access
- closed
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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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