Abstract
Atomistic molecular dynamics (MD) simulations are a vital tool in chemical research, as they are able to provide a view of chemical systems and processes that is not obtainable through experiment. However, large-scale MD simulations require access to multicore clusters or supercomputers that are not always available to all researchers. Recently, many have begun to explore the power of graphics processing units (GPUs) for various applications, such as MD. We present preliminary results of water simulations carried out on GPUs. We compare the performance gained using a GPU versus the same simulation on a single CPU or multiple CPUs. We also address the use of more accurate double precision arithmetic with the newest GPUs and its cost in performance.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
NVIDIA CUDA Programming Guide 2.0, NVIDIA (2008)
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)
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. 28, 2618 (2007)
Anderson, J.A., Lorenz, C.D., Travesset, A.: General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys. 227, 5342 (2008)
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)
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., Kolossváry, 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)
Vlachos, D.G.: A review of multiscale analysis: Examples from systems biology, materials engineering, and other fluid-surface interacting systems. Adv. Chem. Eng. 30, 1–61 (2005)
Yang, J., Wang, Y., Chen, Y.: GPU accelerated molecular dynamics simulation of thermal conductivities. J. Comput. Phys. 221, 799 (2006)
Wu, Y., Tepper, H.L., Voth, G.: Flexible simple point-charge water model with improved liquid-state properties. J. Chem. Phys. 124, 024503 (2006)
Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. Clarendon Press, Oxford (1987)
Nguyen, H. (ed.): GPU Gems 3, ch. 31. Addison-Wesley, Boston (2008)
van Meel, J.A., Arnold, A., Frenkel, D., Zwart, S.F.P., Belleman, R.G.: Harvesting graphics power for MD simulations. Mol. Sim. 34, 259 (2008)
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. 4, 187 (1983)
Lindahl, E., Hess, B., van der Spoel, D.: GROMACS 3.0: A package for molecular simulaton and trajectory analysis. J. Mol. Model. 7, 306 (2001)
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kalé, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781 (2005)
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. 110, 3308 (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Davis, J.E., Ozsoy, A., Patel, S., Taufer, M. (2009). Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors. In: Rajasekaran, S. (eds) Bioinformatics and Computational Biology. BICoB 2009. Lecture Notes in Computer Science(), vol 5462. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00727-9_18
Download citation
DOI: https://doi.org/10.1007/978-3-642-00727-9_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-00726-2
Online ISBN: 978-3-642-00727-9
eBook Packages: Computer ScienceComputer Science (R0)