The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
NAMD: a Parallel, Object-Oriented Molecular Dynamics Program
Abstract
NAMD is a molecular dynamics program designed for high performance simulations of large biomolecular systems on parallel computers. An object-oriented design imple mented using C++ facilitates the incorporation of new algorithms into the program. NAMD uses spatial decom position coupled with a multithreaded, message-driven design, which is shown to scale efficiently to multiple processors. Also, NAMD incorporates the distributed par allel multipole tree algorithm for full electrostatic force evaluation in O( N) time. NAMD can be connected via a communication system to a molecular graphics program in order to provide an interactive modeling tool for viewing and modifying a running simulation. The application of NAMD to a protein-water system of 32,867 atoms illus trates the performance of NAMD.
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Cites
Computer Simulation of Liquids
Allen, M. P., & Tildesley, D. J. (2017) · doi:10.1093/oso/9780198803195.001.0001 · Cited by 20,945
Cited by
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Self-citationScalable 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
Self-citationNature designs tough collagen: Explaining the nanostructure of collagen fibrils
Buehler, M. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603216103 · Cited by 803
Izrailev, S., Stepaniants, S., Isralewitz, B., Kosztin, D., Lu, H., Molnar, F., Wriggers, W., & Schulten, K. (1999) · Lecture Notes in Computational Science and Engineering · doi:10.1007/978-3-642-58360-5_2 · Cited by 451
Self-citationFatigue-resistant adhesion of hydrogels
Liu, J., Lin, S., Liu, X., Qin, Z., Yang, Y., Zang, J., & Zhao, X. (2020) · Nature Communications · doi:10.1038/s41467-020-14871-3 · Cited by 420
Metadata
- Authors
- Nelson, M. T., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L. V., Skeel, R. D., & Schulten, K.
- Venue
- The International Journal of Supercomputer Applications and High Performance Computing
- Publisher
- SAGE Publications
- Published
- 1996-12
- Volume
- 10
- Issue
- 4
- Pages
- 251-268
- ISSN
- 1078-3482 (ISSN-L)
- OpenAlex
- W2156871002
- Cited by
- 559
- References
- 1
- FWCI
- 20.15
- Type
- journal article
- Language
- en
- Open access
- closed
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- Nelson, M. T., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L. V., Skeel, R. D., & Schulten, K. (1996). NAMD: a Parallel, Object-Oriented Molecular Dynamics Program. The International Journal of Supercomputer Applications and High Performance Computing. https://doi.org/10.1177/109434209601000401
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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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