DOI: 10.1016/j.cpc.2008.05.008. Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

10.1016/j.cpc.2008.05.008

Crossref journal-article

Elsevier BV

Computer Physics Communications (78)

Bibliography

Liu, W., Schmidt, B., Voss, G., & MÃ¼ller-Wittig, W. (2008). Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. Computer Physics Communications, 179(9), 634â641.

Authors 4

Weiguo Liu (first)
Bertil Schmidt (additional)
Gerrit Voss (additional)
Wolfgang Müller-Wittig (additional)

References 26 Referenced 124

NVIDIA CUDA Compute Unified Device Architecture-Programming Guide (V1.1), http://developer.download.nvidia.com/compute/cuda/1_1/NVIDIA_CUDA_Programming_Guide_1.1.pdf, Nov. 2007
NVIDIA CUDA Homepage http://developer.nvidia.com/object/cuda.html
10.1109/MC.2007.108 / Computer / Using FPGA devices to accelerate biomolecular simulations by Alam (2007)
M.P. Allen, Introduction to molecular dynamics simulation, in: Computational Soft Matter—From Synthetic Polymers to Proteins, NIC Series, vol. 23, John von Neumann Institute for Computing, 2004, pp. 1–28, http://www.fzj.helmholtz.de/nic-series/volume23/allen.pdf
10.1016/j.cpc.2007.03.004 / Computer Physics Communications / Quantum Monte Carlo on graphical processing units by Anderson (2007)
10.1016/j.jcp.2008.01.047 / Journal of Computational Physics / General purpose molecular dynamics simulations fully implemented on graphics processing units by Anderson (2008)
10.1016/j.newast.2007.07.004 / New Astronomy / High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA by Belleman (2008)
K.J. Bowers, et al., Scalable Algorithms for molecular dynamics simulations on commodity clusters, in: Proc. ACM/IEEE Conf. on Supercomputing (SC06) Tampa, FL, 2006 (10.1145/1188455.1188544)
10.1016/0010-4655(95)00042-E / Computer Physics Communications / GROMACS: A message-passing parallel molecular dynamics implementation by Berendsen (1995)
10.1016/j.cpc.2007.08.013 / Computer Physics Communications / Line-by-line spectroscopy simulations on graphics processing units by Collange (2008)
F. Ercolessi, A molecular dynamics primer, http://www.fisica.uniud.it/~ercolessi/md/, 1997
10.1002/prot.340110403 / Proteins / FASTRUN: A special purpose hardwired computer for molecular simulation by Fine (1991)
{'key': '10.1016/j.cpc.2008.05.008_bib013', 'series-title': 'Proc. International Conf. on Computational Science (ICCS 2006)', 'first-page': '846', 'article-title': 'Blue matter: Strong scaling of molecular dynamics on blue Gene/L', 'volume': 'vol. 3992', 'author': 'Fitch', 'year': '2006'} / Proc. International Conf. on Computational Science (ICCS 2006) / Blue matter: Strong scaling of molecular dynamics on blue Gene/L by Fitch (2006)
{'key': '10.1016/j.cpc.2008.05.008_bib014', 'author': 'Hamada'} by Hamada
{'key': '10.1016/j.cpc.2008.05.008_bib015', 'series-title': 'Proceedings of Physical Society', 'first-page': '461', 'article-title': 'Cohesion', 'author': 'Lennard-Jones', 'year': '1931'} / Proceedings of Physical Society / Cohesion by Lennard-Jones (1931)
10.1109/TPDS.2007.1069 / IEEE Transactions on Parallel and Distributed Systems / Streaming algorithms for biological sequence alignment on GPUs by Liu (2007)
10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B / J. Computational Chemistry / Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function by Morris (1998)
T. Narumi, Y. Ohno, N. Okimoto, A. Suenaga, R. Yanai, M. Taiji, A high-speed special-purpose computer for molecular dynamics simulations: MDGRAPE-3, in: NIC Workshop 2006, NIC Series, vol. 34, John von Neumann Institute for Computing, 2006, pp. 29–36, http://www.fzj.helmholtz.de/nic-series/volume34/narumi.pdf
10.1002/bip.10219 / Biopolymers / Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing by Pande (2003)
10.1006/jcph.1995.1039 / Journal of Computational Physics / Fast parallel algorithms for short-range molecular dynamics by Plimpton (1995)
{'issue': '474', 'key': '10.1016/j.cpc.2008.05.008_bib021', 'article-title': 'High-throughput sequence alignment using graphics processing units', 'volume': '8', 'author': 'Schatz', 'year': '2007', 'journal-title': 'BMC Bioinformatics'} / BMC Bioinformatics / High-throughput sequence alignment using graphics processing units by Schatz (2007)
D.E. Shaw, et al., Anton: A special-purpose machine for molecular dynamics simulation, in: Proceedings of the 34th Annual International Symposium on Computer Architecture, San Diego, California, 2007
10.1002/jcc.20829 / Journal of Computational Chemistry / Accelerating molecular modeling applications with graphics processors by Stone (2007)
10.1109/TPDS.2006.110 / IEEE Transactions on Parallel and Distributed Systems / Predictor@Home: A protein structure prediction supercomputer based on global computing by Taufer (2006)
10.1002/(SICI)1096-987X(19990130)20:2<185::AID-JCC1>3.0.CO;2-L / Journal Computational. Chemistry / Development of MD engine: High-speed accelerator with parallel processor design for molecular dynamics simulations by Toyoda (1999)
10.1016/j.jcp.2006.06.039 / Journal of Computational Physics / GPU accelerated molecular dynamics simulation of thermal conductivities by Yang (2007)

Dates

Type	When
Created	17 years, 2 months ago (June 7, 2008, 4:14 a.m.)
Deposited	6 years, 3 months ago (May 11, 2019, 9:08 p.m.)
Indexed	33 minutes ago (Aug. 28, 2025, 8:10 p.m.)
Issued	16 years, 9 months ago (Nov. 1, 2008)
Published	16 years, 9 months ago (Nov. 1, 2008)
Published Print	16 years, 9 months ago (Nov. 1, 2008)

Funders 0

None

BibTeX

@article{Liu_2008, title={Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA}, volume={179}, ISSN={0010-4655}, url={http://dx.doi.org/10.1016/j.cpc.2008.05.008}, DOI={10.1016/j.cpc.2008.05.008}, number={9}, journal={Computer Physics Communications}, publisher={Elsevier BV}, author={Liu, Weiguo and Schmidt, Bertil and Voss, Gerrit and Müller-Wittig, Wolfgang}, year={2008}, month=nov, pages={634–641} }

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