Abstract
Continuing advances in development of multi-core CPUs, GPUs, and low-cost six-degree-of-freedom virtual reality input devices have created an unprecedented opportunity for broader use of interactive molecular modeling and immersive visualization of large molecular complexes. We describe the design and implementation of VMD, a popular molecular visualization and modeling tool that supports both desktop and immersive virtual reality environments, and includes support for a variety of multi-modal user interaction mechanisms. A number of unique challenges arise in supporting immersive visualization and advanced input devices within software that is used by a broad community of scientists that often have little background in the use or administration of these technologies. We share our experiences in supporting VMD on existing and upcoming low-cost virtual reality hardware platforms, and we give our perspective on how these technologies can be improved and employed to enable next-generation interactive molecular simulation tools for broader use by the molecular modeling community.
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References
Nelson, M., Humphrey, W., Gursoy, A., Dalke, A., Kalé, L., Skeel, R., Schulten, K., Kufrin, R.: MDScope – A visual computing environment for structural biology. In: Atluri, S., Yagawa, G., Cruse, T. (eds.) Computational Mechanics 1995, vol. 1, pp. 476–481 (1995)
Leech, J., Prins, J., Hermans, J.: SMD: Visual steering of molecular dynamics for protein design. IEEE Comp. Sci. Eng. 3, 38–45 (1996)
Humphrey, W., Dalke, A., Schulten, K.: VMD – Visual Molecular Dynamics. J. Mol. Graphics 14, 33–38 (1996)
Ihlenfeldt, W.D.: Virtual reality in chemistry. J. Mol. Mod. 3, 386–402 (1997)
Sharma, R., Zeller, M., Pavlovic, V.I., Huang, T.S., Lo, Z., Chu, S., Zhao, Y., Phillips, J.C., Schulten, K.: Speech/gesture interface to a visual-computing environment. IEEE Comp. Graph. App. 20, 29–37 (2000)
Sankaranarayanan, G., Weghorst, S., Sanner, M., Gillet, A., Olson, A.: Role of haptics in teaching structural molecular biology. In: International Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems, p. 363 (2003)
Cruz-Neira, C., Sandin, D.J., DeFanti, T.A.: Surround-screen projection-based virtual reality: The design and implementation of the CAVE. In: Proceedings of SIGGRAPH 1993, Anaheim, CA,, pp. 135–142. ACM, New York (1993)
Czernuszenko, M., Pape, D., Sandin, D., DeFanti, T., Dawe, G.L., Brown, M.D.: The ImmersaDesk and Infinity Wall projection-based virtual reality displays. SIGGRAPH Comput. Graph. 31, 46–49 (1997)
Pape, D., Anstey, J., Sherman, B.: Commodity-based projection VR. In: SIGGRAPH 2004: ACM SIGGRAPH 2004 Course Notes, p. 19. ACM, New York (2004)
Taylor II, R.M., Hudson, T.C., Seeger, A., Weber, H., Juliano, J., Helser, A.T.: VRPN: a device-independent, network-transparent VR peripheral system. In: VRST 2001: Proceedings of the ACM Symposium on Virtual Reality Software and Technology, pp. 55–61. ACM, New York (2001)
Bierbaum, A., Just, C., Hartling, P., Meinert, K., Baker, A., Cruz-Neira, C.: VR Juggler: a virtual platform for virtual reality application development. In: Proceedings of IEEE Virtual Reality, pp. 89–96 (2001)
Martens, J.B., Qi, W., Aliakseyeu, D., Kok, A.J.F., van Liere, R.: Experiencing 3D interactions in virtual reality and augmented reality. In: EUSAI 2004: Proceedings of the 2nd European Union Symposium on Ambient Intelligence, pp. 25–28. ACM, New York (2004)
Stone, J., 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, New York. ACM SIGGRAPH, pp. 191–194 (2001)
Kreylos, O.: Environment-independent VR development. 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. 901–912. Springer, Heidelberg (2008)
Angus, I.G., Sowizral, H.A.: Embedding the 2D interaction metaphor in a real 3D virtual environment, vol. 2409, pp. 282–293. SPIE, San Jose (1995)
Watsen, K., Darken, R.P., Capps, M.V.: A handheld computer as an interaction device to a virtual environment. In: Proceedings of the Third Immersive Projection Technology Workshop (1999)
Hartling, P.L., Bierbaum, A.D., Cruz-Niera, C.: Tweek: Merging 2D and 3D interaction in immersive environments. In: Proceedings of the 6th World Multiconference on Systemics, Cybernetics, and Informatics, Orlando, FL, USA, vol. VI, pp. 1–5 (2002)
Férey, N., Delalande, O., Grasseau, G., Baaden, M.: A VR framework for interacting with molecular simulations. In: VRST 2008: Proceedings of the 2008 ACM Symposium on Virtual Reality Software and Technology, pp. 91–94. ACM, New York (2008)
Grayson, P., Tajkhorshid, E., Schulten, K.: Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. Biophys. J. 85, 36–48 (2003)
Hamdi, M., Ferreira, A., Sharma, G., Mavroidis, C.: Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality. Microelectronics Journal 39, 190–201 (2008)
Phillips, J.C., Stone, J.E., Schulten, K.: Adapting a message-driven parallel application to GPU-accelerated clusters. In: SC 2008: Proceedings of the 2008 ACM/IEEE Conference on Supercomputing, Piscataway, NJ, USA. IEEE Press, Los Alamitos (2008)
Anderson, J.A., Lorenz, C.D., Travesset, A.: General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Chem. Phys. 227, 5342–5359 (2008)
Stone, J.E., Hardy, D.J., Ufimtsev, I.S., Schulten, K.: GPU-accelerated molecular modeling coming of age. J. Mol. Graph. Model. 29, 116–125 (2010)
Hachet, M., Kitamura, Y.: 3D interaction with and from handheld computers. In: Proceedings of IEEE VR 2005 Workshop: New Directions in 3D User Interfaces. IEEE, Los Alamitos (2005)
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Stone, J.E., Kohlmeyer, A., Vandivort, K.L., Schulten, K. (2010). Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware. In: Bebis, G., et al. Advances in Visual Computing. ISVC 2010. Lecture Notes in Computer Science, vol 6454. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-17274-8_38
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DOI: https://doi.org/10.1007/978-3-642-17274-8_38
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