{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T16:50:49Z","timestamp":1774371049195,"version":"3.50.1"},"publisher-location":"Berlin, Heidelberg","reference-count":16,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783642007262","type":"print"},{"value":"9783642007279","type":"electronic"}],"license":[{"start":{"date-parts":[[2009,1,1]],"date-time":"2009-01-01T00:00:00Z","timestamp":1230768000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009]]},"DOI":"10.1007\/978-3-642-00727-9_18","type":"book-chapter","created":{"date-parts":[[2009,4,21]],"date-time":"2009-04-21T00:45:52Z","timestamp":1240274752000},"page":"176-186","source":"Crossref","is-referenced-by-count":6,"title":["Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors"],"prefix":"10.1007","author":[{"given":"Joseph E.","family":"Davis","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adnan","family":"Ozsoy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandeep","family":"Patel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michela","family":"Taufer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"18_CR1","unstructured":"NVIDIA CUDA Programming Guide 2.0, NVIDIA (2008)"},{"key":"18_CR2","doi-asserted-by":"crossref","unstructured":"Stone, S.S., Haldar, J.P., Tsao, S.C., Hwu, W.W., Liang, Z., Sutton, B.P.: Accelerating advanced MRI reconstructions on GPUs. In: Proc. of 2008 Computing Frontiers Conference, May 7-9 (2008)","DOI":"10.1145\/1366230.1366276"},{"key":"18_CR3","doi-asserted-by":"publisher","first-page":"2618","DOI":"10.1002\/jcc.20829","volume":"28","author":"J.E. Stone","year":"2007","unstructured":"Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., Schulten, K.: Accelerating molecular modeling applications with graphics processors. J. Comput. Chem.\u00a028, 2618 (2007)","journal-title":"J. Comput. Chem."},{"key":"18_CR4","doi-asserted-by":"publisher","first-page":"5342","DOI":"10.1016\/j.jcp.2008.01.047","volume":"227","author":"J.A. Anderson","year":"2008","unstructured":"Anderson, J.A., Lorenz, C.D., Travesset, A.: General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys.\u00a0227, 5342 (2008)","journal-title":"J. Comput. Phys."},{"key":"18_CR5","doi-asserted-by":"crossref","unstructured":"Taiji, M., Narumi, T., Ohno, Y., Futatsugi, N., Suenaga, A., Takada, N., Konagaya, A.: Protein Explorer: A petaflops special-purpose computer system for molecular dynamics simulations. In: Proc. of 2003 ACM\/IEEE Supercomputing Conference, November 15-21 (2003)","DOI":"10.1145\/1048935.1050166"},{"key":"18_CR6","doi-asserted-by":"crossref","unstructured":"Shaw, D.E., Deneroff, M.M., Dror, R.O., Kuskin, J.S., Larson, R.H., Salmon, J.K., Young, C., Batson, B., Bowers, K.J., Chao, J.C., Eastwood, M.P., Gagliardo, J., Grossman, J.P., Ho, C.R., Ierardi, D.J., Kolossv\u00e1ry, I., Klepeis, J.L., Layman, T., McLeavey, C., Moraes, M.A., Mueller, R., Priest, E.C., Shan, Y., Spengler, J., Theobald, M., Towles, B., Wang, S.C.: Anton: A special-purpose machine for molecular dynamics simulation. In: Proc. of the 34th Annual International Symposium on Computer Architecture, June 9-13 (2007)","DOI":"10.1145\/1250662.1250664"},{"key":"18_CR7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0065-2377(05)30001-9","volume":"30","author":"D.G. Vlachos","year":"2005","unstructured":"Vlachos, D.G.: A review of multiscale analysis: Examples from systems biology, materials engineering, and other fluid-surface interacting systems. Adv. Chem. Eng.\u00a030, 1\u201361 (2005)","journal-title":"Adv. Chem. Eng."},{"key":"18_CR8","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1016\/j.jcp.2006.06.039","volume":"221","author":"J. Yang","year":"2006","unstructured":"Yang, J., Wang, Y., Chen, Y.: GPU accelerated molecular dynamics simulation of thermal conductivities. J. Comput. Phys.\u00a0221, 799 (2006)","journal-title":"J. Comput. Phys."},{"key":"18_CR9","doi-asserted-by":"publisher","first-page":"24503","DOI":"10.1063\/1.2136877","volume":"124","author":"Y. Wu","year":"2006","unstructured":"Wu, Y., Tepper, H.L., Voth, G.: Flexible simple point-charge water model with improved liquid-state properties. J. Chem. Phys.\u00a0124, 024503 (2006)","journal-title":"J. Chem. Phys."},{"key":"18_CR10","volume-title":"Computer Simulation of Liquids","author":"M.P. Allen","year":"1987","unstructured":"Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. Clarendon Press, Oxford (1987)"},{"key":"18_CR11","volume-title":"GPU Gems 3","year":"2008","unstructured":"Nguyen, H. (ed.): GPU Gems 3, ch.\u00a031. Addison-Wesley, Boston (2008)"},{"key":"18_CR12","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1080\/08927020701744295","volume":"34","author":"J.A. Meel van","year":"2008","unstructured":"van Meel, J.A., Arnold, A., Frenkel, D., Zwart, S.F.P., Belleman, R.G.: Harvesting graphics power for MD simulations. Mol. Sim.\u00a034, 259 (2008)","journal-title":"Mol. Sim."},{"key":"18_CR13","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/jcc.540040211","volume":"4","author":"B.R. Brooks","year":"1983","unstructured":"Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M.: CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem.\u00a04, 187 (1983)","journal-title":"J. Comput. Chem."},{"key":"18_CR14","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1007\/s008940100045","volume":"7","author":"E. Lindahl","year":"2001","unstructured":"Lindahl, E., Hess, B., van der Spoel, D.: GROMACS 3.0: A package for molecular simulaton and trajectory analysis. J. Mol. Model.\u00a07, 306 (2001)","journal-title":"J. Mol. Model."},{"key":"18_CR15","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"J.C. Phillips","year":"2005","unstructured":"Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kal\u00e9, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Comput. Chem.\u00a026, 1781 (2005)","journal-title":"J. Comput. Chem."},{"key":"18_CR16","doi-asserted-by":"publisher","first-page":"3308","DOI":"10.1021\/jp056043p","volume":"110","author":"G. Lamoureux","year":"2006","unstructured":"Lamoureux, G., Roux, B.: Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. J. Phys. Chem. B.\u00a0110, 3308 (2006)","journal-title":"J. Phys. Chem. B."}],"container-title":["Lecture Notes in Computer Science","Bioinformatics and Computational Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-00727-9_18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,12]],"date-time":"2018-10-12T03:24:20Z","timestamp":1539314660000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-00727-9_18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009]]},"ISBN":["9783642007262","9783642007279"],"references-count":16,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-00727-9_18","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009]]}}}