Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 919

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

Open access
Harvey, M. J., Giupponi, G., Fabritiis, G. De·2009·Journal of Chemical Theory and Computation
DOI 10.1021/ct9000685
Open this paper in CoChat — free account

Abstract

The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER force fields. Designed specifically for GPUs it is able to achieve supercomputing scale performance of 40 ns/day for all-atom protein systems with over 23 000 atoms. We provide a validation and performance evaluation of the code and run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. We believe that microsecond time scale molecular dynamics on cost-effective hardware will have important methodological and scientific implications.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1021/ct9000685

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 38

  1. Giupponi G., 2008, Drug Discovery Today, 13, 1052, 10.1016/j.drudis.2008.08.001 · DOI
  2. Shaw D. E., 2007, Proceedings of the 34th annual international symposium on Computer architecture
  3. Bowers K. J., 2006, J. Chem. Phys., 24, 184109, 10.1063/1.2191489 · DOI
  4. Bowers K. J., 2005, J. Phys.: Conf. Ser., 16, 300
  5. Bowers K. J., 2006, Proceedings of ACM/IEEE Conference on SuperComputing 2006
  6. Hess B., 2008, J. Chem. Theor. Comput., 4, 435, 10.1021/ct700301q · DOI · Paper page
  7. De Fabritiis G., 2007, Comput. Phys. Commun., 176, 600, 10.1016/j.cpc.2007.02.107 · DOI
  8. Luttmann E., 2008, J. Comput. Chem., 30, 268, 10.1002/jcc.21054 · DOI
  9. Shirts M., 2000, Science, 290, 1903, 10.1126/science.290.5498.1903 · DOI · Paper page
  10. Harvey M. J., Distributed & Grid Computing-Science Made Transparent for Everyone. Principles, Applications and Supporting Communities
  11. Anderson D., 2009, Bekeley Open Infrastructure for Network Computing
  12. 2009, OpenGL-The Industry Standard for High Performance Graphics
  13. Nickolls J., 2008, ACM Queue, 6, 10.1145/1365490.1365500 · DOI · Paper page
  14. Stone J., 2007, J. Comput. Chem., 28, 2618, 10.1002/jcc.20829 · DOI · Paper page
  15. van Meel J. A., 2008, Mol. Simul.
  16. Phillips J. C., 2008, Proceedings of the 2008 ACM/IEEE Conference on Supercomputing
  17. Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; LeGrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. 2009, 30, 864–872 · DOI · Paper page
  18. Ufimtsev I., 2008, J. Chem. Theory Comput., 4, 222, 10.1021/ct700268q · DOI · Paper page
  19. Anderson A. G., 2008, Comput. Phys. Commun., 177, 298, 10.1016/j.cpc.2007.03.004 · DOI
  20. Vogt L., 2008, J. Phys. Chem. A, 112, 2049, 10.1021/jp0776762 · DOI
  21. Yasuda K., 2008, J. Chem. Theor. Comput., 4, 1230, 10.1021/ct8001046 · DOI
  22. Ewald P., 1921, Ann. Phys., 64, 253, 10.1002/andp.19213690304 · DOI · Paper page
  23. MacKerell A. D., 1998, J. Phys. Chem. B, 102, 3586, 10.1021/jp973084f · DOI · Paper page
  24. Ponder J. W., 2003, Adv. Protein Chem., 66, 27, 10.1016/S0065-3233(03)66002-X · DOI · Paper page
  25. Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R. A.; Parrinello, M.PLUMED: a portable plugin for free-energy calculations with molecular dynamics; 2009. · DOI · Paper page
  26. Essman U., 1995, J. Chem. Phys., 19, 8577, 10.1063/1.470117 · DOI · Paper page
  27. Feenstra K. A., 1999, J. Comput. Chem., 20, 786, 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B · DOI · Paper page
  28. Hardy D. J., 2007, MDX libraries
  29. Kräutler V., 2001, J. Comput. Chem., 22, 501, 10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V · DOI · Paper page
  30. Andersen H. C., 1983, J. Comput. Phys., 52, 24, 10.1016/0021-9991(83)90014-1 · DOI · Paper page
  31. Verlet L., 1967, Part. Part. Syst. Charact., 159, 98
  32. Feenstra K., 1999, J. Comput. Chem., 20, 786, 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B · DOI · Paper page
  33. Lippert R. A., 2007, J. Chem. Phys., 126, 046101, 10.1063/1.2431176 · DOI
  34. Tironi I. G., J. Chem. Phys., 102, 5451, 10.1063/1.469273 · DOI · Paper page
  35. Plimpton S., 1996, J. Comput. Chem., 17, 326, 10.1002/(SICI)1096-987X(199602)17:3<326::AID-JCC7>3.0.CO;2-X · doi:10.1002/(sici)1096-987x(199602)17:3<326::aid-jcc7>3.0.co;2-x
  36. Ensign D., 2007, J. Mol. Biol., 374, 806, 10.1016/j.jmb.2007.09.069 · DOI
  37. Anderson D. L., 2004, Proceedings of Fifth IEEE/ACM International Workshop on Grid Computing (GRID’04)
  38. Holden C., 2008, Science, 321, 1425

Cited by

See all 919

Metadata

Authors
Harvey, M. J., Giupponi, G., & Fabritiis, G. D.
Venue
Journal of Chemical Theory and Computation
Publisher
American Chemical Society (ACS)
Published
2009-05-21
Volume
5
Issue
6
Pages
1632-1639
ISSN
  • 1549-9618 (ISSN-L)
  • 1549-9626
DOI
10.1021/ct9000685
OpenAlex
W2082586732
Cited by
919
References
3
FWCI
47.51
Type
journal article
Language
en
Open access
green

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.