Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories

  • John E. Stone
  • Kirby L. Vandivort
  • Klaus Schulten
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6939)


Atomistic molecular dynamics (MD) simulations of biomolecules provide insight into their physical mechanisms and potential as drug targets. Unfortunately, such simulations are extremely demanding in terms of computation, storage, and visualization. Immersive visualization environments permit fast, intuitive exploration of the pharmacological potential, but add further demands on resources. We describe the design and application of out-of-core visualization techniques for large-size and long-timescale MD simulations involving many terabytes of data, including in particular: fast regeneration of molecular representations, atom selection mechanisms, out-of-core optimized MD trajectory file formats, and multithreaded programming techniques. Our approach leverages technological advances in commodity solid state disk (SSD) devices, to enable trajectory animation rates for large structures that were previously unachievable except by in-core approaches, while maintaining full visualization flexibility. The out-of-core visualization techniques are implemented and evaluated in VMD, a widely used molecular visualization tool.


Molecular Dynamic Trajectory Trajectory Data Trajectory Format Atomistic Molecular Dynamic Molecular Visualization 
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  1. 1.
    Kreylos, O., Bawden, G.W., Kellogg, L.H.: Immersive visualization and analysis of LiDAR data. In: Bebis, G., Boyle, R., Parvin, B., Koracin, D., Remagnino, P., Porikli, F., Peters, J., Klosowski, J., Arns, L., Chun, Y.K., Rhyne, T.-M., Monroe, L. (eds.) ISVC 2008, Part I. LNCS, vol. 5358, pp. 846–855. Springer, Heidelberg (2008)CrossRefGoogle Scholar
  2. 2.
    Kuester, F., Bruckschen, R., Hamann, B., Joy, K.I.: Visualization of particle traces in virtual environments. In: Proceedings of the ACM Symposium on Virtual Reality Software and Technology, VRST 2001, pp. 151–157. ACM, New York (2001)Google Scholar
  3. 3.
    Gao, Y., Deng, B., Wu, L.: Efficient view-dependent out-of-core rendering of large-scale and complex scenes. In: Proceedings of the 2006 ACM International Conference on Virtual Reality Continuum and its Applications. VRCIA 2006, pp. 297–303. ACM, New York (2006)CrossRefGoogle Scholar
  4. 4.
    Grottel, S., Reina, G., Dachsbacher, C., Ertl, T.: Coherent culling and shading for large molecular dynamics visualization. Computer Graphics Forum (Proceedings of EUROVIS 2010) 29, 953–962 (2010)CrossRefGoogle Scholar
  5. 5.
    Humphrey, W., Dalke, A., Schulten, K.: VMD – Visual Molecular Dynamics. J. Mol. Graphics 14, 33–38 (1996)CrossRefGoogle Scholar
  6. 6.
    Stone, J.E., Kohlmeyer, A., Vandivort, K.L., Schulten, K.: Immersive molecular visualization and interactive modeling with commodity hardware. In: Bebis, G., Boyle, R., Parvin, B., Koracin, D., Chung, R., Hammound, R., Hussain, M., Kar-Han, T., Crawfis, R., Thalmann, D., Kao, D., Avila, L. (eds.) ISVC 2010. LNCS, vol. 6454, pp. 382–393. Springer, Heidelberg (2010)CrossRefGoogle Scholar
  7. 7.
    Tarini, M., Cignoni, P., Montani, C.: Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics 12, 1237–1244 (2006)CrossRefGoogle Scholar
  8. 8.
    Chavent, M., Levy, B., Maigret, B.: MetaMol: High-quality visualization of molecular skin surface. J. Mol. Graph. Model. 27, 209–216 (2008)CrossRefGoogle Scholar
  9. 9.
    Stone, J.E., Saam, J., Hardy, D.J., Vandivort, K.L., Hwu, W.W., Schulten, K.: High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs. In: Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units. ACM International Conference Proceeding Series, vol. 383, pp. 9–18. ACM, New York (2009)Google Scholar
  10. 10.
    Krone, M., Bidmon, K., Ertl, T.: Interactive visualization of molecular surface dynamics. IEEE Transactions on Visualization and Computer Graphics 15, 1391–1398 (2009)CrossRefGoogle Scholar
  11. 11.
    Chavent, M., Levy, B., Krone, M., Bidmon, K., Nomine, J.P., Ertl, T., Baaden, M.: GPU-powered tools boost molecular visualization. Briefings in Bioinformatics (2011)Google Scholar
  12. 12.
    Arcangeli, A.: O_DIRECT. In: Proceedings of the UKUUG Linux 2001 Linux Developer’s Conference (2001)Google Scholar
  13. 13.
    Stone, J.E., Gullingsrud, J., Grayson, P., Schulten, K.: A system for interactive molecular dynamics simulation. In: Hughes, J.F., Séquin, C.H. (eds.) 2001 ACM Symposium on Interactive 3D Graphics, ACM SIGGRAPH, New York, pp. 191–194 (2001)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • John E. Stone
    • 1
  • Kirby L. Vandivort
    • 1
  • Klaus Schulten
    • 1
    • 2
  1. 1.Beckman Institute for Advanced Science and TechnologyUniversity of IllinoisUrbana-ChampaignUSA
  2. 2.Department of PhysicsUniversity of IllinoisUrbana-ChampaignUSA

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