Interactive molecular dynamics: Scaling up to large systems

Procedia Computer Science

Volumn 18, Issue , 2013, Pages 20-29

  Dreher, Matthieu ^a   Piuzzi, Marc ^b   Turki, Ahmed ^c   Chavent, Matthieu ^b   Baaden, Marc ^b   Férey, Nicolas ^d   Limet, Sébastien ^c   Raffin, Bruno ^a   Robert, Sophie ^c  

^a INRIA   (France)

^b France   (France)

^c UNIVERSITÉ D'ORLÉANS   (France)

^d UFR 919 Laboratoire d'Informatique Pour la Mécanique et les Sciences de l'Ingénieur   (France)

Author keywords

Computational steering with haptic arm; High performance interactive computing; Interactive molecular dynamics

Indexed keywords

EID: 84888328737     PISSN: 18770509     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1016/j.procs.2013.05.165     Document Type: Conference Paper

References (23)

1. J. Allard, J.-D. Lesage, and B. Raffin. Modularity for Large Virtual Reality Applications. Presence: Teleoperators and Virtual Environments, 19(2):142-162, April 2010.
2. A. Anderson and Z. Weng. VRDD: Applying virtual reality visualization to protein docking and design. Journal of Molecular Graphics and Modelling, 17(34):180 - 186, 1999.
3. P. Bivall Persson, L. Tibell, M. Cooper, A. Ynnerman, and B.-H. Jonsson. Evaluating the Effectiveness of Haptic Visualization in Biomolecular Education - Feeling Molecular Specificity in a Docking Task. In 12th IOSTE Symposium, pages 745-752. Universiti Science Malaysia, 2006.
4. F. P. Brooks Jr., M. Ouh-Young, J. J. Batter, and P. Jerome Kilpatrick. Project GROPEHaptic displays for scientific visualization. In Proceedings of Siggraph '90, pages 177-185, New York, NY, USA, 1990. ACM.
5. M. Chavent, A. Vanel, A. Tek, B. Levy, S. Robert, B. Raffin, and M. Baaden. GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids. Journal of Computational Chemistry, 32(13):2924-2935, 2011.
6. J. Esque, M. Sansom, M. Baaden, and C. Oguey. A case study of protein topology: how enterobactin modifies the water network through fepA. submitted to PLoS One.
7. S. Grottel, G. Reina, C. Dachsbacher, and T. Ertl. Coherent Culling and Shading for Large Molecular Dynamics Visualization. Computer Graphics Forum, 29(3):953-962, 2010.
8. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Journal of Chemical Theory and Computation, 4(3):435-447, 2008.
9. W. Humphrey, A. Dalke, and K. Schulten. VMD - Visual Molecular Dynamics. Journal of Molecular Graphics, 14:33-38, 1996.
10. J. Insley, M. Papka, S. Dong, G. Karniadakis, and N. Karonis. Runtime Visualization of the Human Arterial Tree. Visualization and Computer Graphics, IEEE Transactions on, 13(4):810 -821, july-aug. 2007.
11. S. Izrailev, S. Stepaniants, B. Isralewitz, D. Kosztin, H. Lu, F. Molnar, W. Wriggers, and K. Schulten. Steered Molecular Dynamics. In Computational Molecular Dynamics: Challenges, Methods, Ideas, pages 39-65. Springer-Verlag, 1998.
12. M. Koutek, J. van Hees, F. H. Post, and A. F. Bakker. Virtual spring manipulators for particle steering in molecular dynamics on the responsive workbench. In Proceedings of EGVE '02, pages 53-ff, Aire-la-Ville, Switzerland, 2002. Eurographics Association.
13. M. Krone, J. E. Stone, T. Ertl, and K. Schulten. Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. In EuroVis 2012 Short Papers, volume 1, 2012.
14. J.-D. Lesage and B. Raffin. A Hierarchical Component Model for Large Parallel Interactive Applications. Journal of Supercomputing, 60:389-409, June 2012.
15. M. D. Mazzeo, S. Manos, and P. V. Coveney. In situ ray tracing and computational steering for interactive blood flow simulation. Computer Physics Communications, 181(2):355 - 370, 2010.
16. S. Parker, D. Weinstein, and C. Johnson. The SCIRun Computational Steering Software system. In E. Arge, A. Bruaset, and H. Langtangen, editors, Modern Software Tools in Scientific Computing, pages 1-40. Birkhauser Press, Boston, 1997.
17. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kal, and K. Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16):1781-1802, 2005.
18. L. Renambot, H. E. Bal, D. Germans, and H. J. W. Spoelder. CAVEStudy: An Infrastructure for Computational Steering and Measuring in Virtual Reality Environments. Cluster Computing, 4(1):79-87, Mar. 2001.
19. Schrödinger, LLC. The PyMOL Molecular Graphics System, Version 1.3r1. August 2010.
20. J. E. Stone, J. Gullingsrud, and K. Schulten. A system for interactive molecular dynamics simulation. In Proceedings of the 2001 symposium on Interactive 3D graphics, I3D '01, pages 191-194, New York, NY, USA, 2001. ACM.
21. J. E. Stone, A. Kohlmeyer, K. L. Vandivort, and K. Schulten. Immersive molecular visualization and interactive modeling with commodity hardware. In Proceedings ISVC'10, pages 382-393, Berlin, Heidelberg, 2010. Springer-Verlag.
22. R. M. Taylor II, R. M. T. Li, T. C. Hudson, A. Seeger, H. Weber, J. Juliano, and A. T. Helser. VRPN: A Device-Independent, Network- Transparent VR Peripheral System, 2001.
23. R. van Liere, J. D. Mulder, and J. J. V. Wijk. Computational Steering, 1996.