Advertisement

GPU Computing in Biomolecular Modeling and Nanodesign

  • Tibor Kožár
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7125)

Abstract

In addition to the intended use of graphics processing units (GPU) to accelerate computer games, their potential has become apparent for scientific computations in the recent years. Molecular modeling and molecular design are only few examples of numerous research areas that are significantly benefiting from novel developments of hardware and software platforms. For example, the impact of high computational power of GPUs has been demonstrated in molecular dynamics (MD) simulations or quantum chemical (QC) calculations. Thus far, several MD programs have been adapted to GPU computing, including NAMD/VMD, GROMACS, AMBER, etc. In addition, modeling tools intended for molecular design based on receptor-ligand interactions, such as molecular docking or core hopping protocols have recently been updated for GPU environment. The tremendous increase in the computing power facilitated by the integration of GPUs and the availability of GPU-based systems could accelerate material research on nanoscale. The price/performance ratio of GPU-based systems supports the development of custom-made protocols for efficient modeling of biomolecular systems and nanostructures. GPU-related molecular modeling tools will also accelerate the combined quantum chemical/molecular mechanics (QC/MM) methodologies. An overview of the performance of NVIDIA Tesla GPU-based system built for high-performance and high-throughput computing aimed for biomolecular modeling and nanodesign is presented.

Keywords

GPU computing molecular modeling molecular dynamics simulations 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Allinger, N.L.: J. Am. Chem. Soc. 99, 8127–8134 (1977)CrossRefGoogle Scholar
  2. 2.
    Allinger, N.L., Chen, K.H., Lii, J.H., Durkin, K.A.: J. Comput. Chem. 24, 1447–1472 (2003)CrossRefGoogle Scholar
  3. 3.
    Allinger, N.L., Fan, Y.: J. Comput. Chem. 18, 1827–1847 (1997)CrossRefGoogle Scholar
  4. 4.
    Allinger, N.L., Yuh, Y.H., Lii, J.-H.: J. Am. Chem. Soc. 111, 8551–8566 (1989)CrossRefGoogle Scholar
  5. 5.
    Anderson, A.G., Goddard, W.A., Schroder, P.: Comput. Phys. Commun. 177, 298–306 (2007)CrossRefGoogle Scholar
  6. 6.
    Anderson, J.A., Lorenz, C.D., Travesset, A.: J. Comput. Phys. 227, 5342–5359 (2008)CrossRefGoogle Scholar
  7. 7.
    Arnautova, Y.A., Jagielska, A., Scheraga, H.A.: J. Phys. Chem. B 110, 5025–5044 (2006)CrossRefGoogle Scholar
  8. 8.
    Brooks, B.R., Brooks III, C.L., Mackerell Jr., A.D., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A.R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R.W., Post, C.B., Pu, J.Z., Schaefer, M., Tidor, B., Venable, R.M., Woodcock, H.L., Wu, X., Yang, W., York, D.M., Karplus, M.: J. Comput. Chem. 30, 1545–1614 (2009)CrossRefGoogle Scholar
  9. 9.
    Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M.: J. Comput. Chem. 4, 187–217 (1983)CrossRefGoogle Scholar
  10. 10.
    Case, D.A., Darden, T.A., Cheatham III, T.E., Simmerling, C.L., Wang, J., Duke, R.E., Luo, R., Walker, R.C., Zhang, W., Merz, K.M., Roberts, B., Wang, B., Hayik, S., Roitberg, A., Seabra, G., Kolossvry, I., Wong, K.F., Paesani, F., Vanicek, J., Wu, X., Brozell, S.R., Steinbrecher, T., Gohlke, H., Cai, Q., Ye, X., Wang, J., Hsieh, M.-J., Cui, G., Roe, D.R., Mathews, D.H., Seetin, M.G., Sagui, C., Babin, V., Luchko, T., Gusarov, S., Kovalenko, A., Kollman, P.A.: Amber 11. University of California, San Francisco (2010)Google Scholar
  11. 11.
    De Fabritiis, G.: Comput. Phys. Commun. 176, 660–664 (2007)CrossRefGoogle Scholar
  12. 12.
    Freddolino, P.L., Arkhipov, A.S., Larson, S.B., McPherson, A., Schulten, K.: Structure 14, 437–449 (2006)CrossRefGoogle Scholar
  13. 13.
    Gordon, M., Schmidt, M.: Theory and Applications of Computational Chemistry: the first forty years. In: Dykstra, C.E., Frenking, G., Kim, K.S., Scuseria, G.E. (eds.), pp. 1167–1189Google Scholar
  14. 14.
    Hagler, A.T., Huler, E., Lifson, S.: J. Am. Chem. Soc. 96, 5319–5327 (1974)CrossRefGoogle Scholar
  15. 15.
    Harvey, M.J., Giupponi, G., De Fabritiis, G.: J. Chem. Theory Comput. 5, 1632–1639 (2009)CrossRefGoogle Scholar
  16. 16.
    Humphrey, W., Dalke, A., Schulten, K.: J. Mol. Graph. 14, 33–38, 27–38 (1996)CrossRefGoogle Scholar
  17. 17.
    Jaguar, version 7.0. Schrodinger, LLC., New York, NY, USA (2008)Google Scholar
  18. 18.
    Lii, J.-H., Allinger, N.L.: J. Am. Chem. Soc. 111, 8566–8575 (1989)CrossRefGoogle Scholar
  19. 19.
    Lii, J.-H., Allinger, N.L.: J. Am. Chem. Soc. 111, 8576–8582 (1989)CrossRefGoogle Scholar
  20. 20.
    Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W.: Molecular Dynamics Simulations on Commodity GPUs with CUDA. In: Aluru, S., Parashar, M., Badrinath, R., Prasanna, V.K. (eds.) HiPC 2007. LNCS, vol. 4873, pp. 185–196. Springer, Heidelberg (2007)CrossRefGoogle Scholar
  21. 21.
    Ma, W., Krishnamoorthy, S., Villa, O., Kowalski, K.: J. Chem. Theory Comput. 7, 1316–1327 (2011)CrossRefGoogle Scholar
  22. 22.
    MacKerell, A.D., Brooks, B., Brooks, C.L., Nilsson, L., Roux, B., Won, Y., Karplus, M.: Charmm: The energy function and its parameterization. In: Encyclopedia of Computational Chemistry. John Wiley & Sons, Ltd. (2002)Google Scholar
  23. 23.
    Martinez, T.J., Ufimtsev, I.S.: J. Chem. Theory Comput. 4, 222–231 (2008)CrossRefGoogle Scholar
  24. 24.
    Martinez, T.J., Ufimtsev, I.S.: J. Chem. Theory Comput. 5, 2619–2628 (2009)CrossRefGoogle Scholar
  25. 25.
    Nemethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S., Scheraga, H.A.: J. Phys Chem-Us 96, 6472–6484 (1992)CrossRefGoogle Scholar
  26. 26.
    Nemethy, G., Pottle, M.S., Scheraga, H.A.: J. Phys. Chem-Us 87, 1883–1887 (1983)CrossRefGoogle Scholar
  27. 27.
    Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., Schulten, K.: J. Comput. Chem. 26, 1781–1802 (2005)CrossRefGoogle Scholar
  28. 28.
    Phillips, J.C., Stone, J.E.: Commun. ACM 52, 34–41 (2009)CrossRefGoogle Scholar
  29. 29.
    Ritchie, D.W.: Proteins 52, 98–106 (2003)CrossRefGoogle Scholar
  30. 30.
    Schatz, M.C., Trapnell, C., Delcher, A.L., Varshney, A.: BMC Bioinformatics 8, 474 (2007)CrossRefGoogle Scholar
  31. 31.
    Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, S.: J. Comput. Chem. 14, 1347–1363 (1993)CrossRefGoogle Scholar
  32. 32.
    Schulten, K., Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G.: J. Comput. Chem. 28, 2618–2640 (2007)CrossRefGoogle Scholar
  33. 33.
    Stone, J.E., Hardy, D.J., Ufimtsev, I.S., Schulten, K.: J. Mol. Graph. Model. 29, 116–125 (2010)CrossRefGoogle Scholar
  34. 34.
    Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., Schulten, K.: J. Comput. Chem. 28, 2618–2640 (2007)CrossRefGoogle Scholar
  35. 35.
    Uejima, Y., Terashima, T., Maezono, R.: J. Comput. Chem. 32, 2264–2272 (2011)CrossRefGoogle Scholar
  36. 36.
    Ufimtsev, I.S., Martinez, T.J.: Comp. Sci. Eng. 10, 26–34 (2008)CrossRefGoogle Scholar
  37. 37.
    Ufimtsev, I.S., Martinez, T.J.: J. Chem. Theory Comput. 5, 1004–1015 (2009)CrossRefGoogle Scholar
  38. 38.
    Valiev, M., Bylaska, E.J., Govind, N., Kowalski, K., Straatsma, T.P., Van Dam, H.J.J., Wang, D., Nieplocha, J., Apra, E., Windus, T.L., de Jong, W.A.: Comput. Phys. Commun. 181, 1477–1489 (2010)CrossRefGoogle Scholar
  39. 39.
    Van Gunsteren, W., Berendsen, H.: University of Groningen, The Netherlands (1987)Google Scholar
  40. 40.
    Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: J. Comput. Chem. 25, 1157–1174 (2004)CrossRefGoogle Scholar
  41. 41.
    Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., Weiner, P.: J. Am. Chem. Soc. 106, 765–784 (1984)CrossRefGoogle Scholar
  42. 42.
    Wilkinson, K.A., Sherwood, P., Guest, M.F., Naidoo, K.J.: J. Comput. Chem. 32, 2313–2318 (2011)CrossRefGoogle Scholar
  43. 43.
    Yang, L., Tan, C.H., Hsieh, M.J., Wang, J., Duan, Y., Cieplak, P., Caldwell, J., Kollman, P.A., Luo, R.: J. Phys. Chem. B 110, 13166–13176 (2006)CrossRefGoogle Scholar
  44. 44.
    Yarovsky, I., Makarucha, A.J., Todorova, N.: European Biophysics Journal with Biophysics Letters 40, 103–115 (2011)CrossRefGoogle Scholar
  45. 45.
    Zimmerman, S.S., Pottle, M.S., Nemethy, G., Scheraga, H.A.: Macromolecules 10, 1–9 (1977)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Tibor Kožár
    • 1
  1. 1.Department of Biophysics, Institute of Experimental PhysicsSlovak Academy of SciencesKošiceSlovakia

Personalised recommendations