Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware

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.

[1]  Marc Baaden,et al.  A VR framework for interacting with molecular simulations , 2008, VRST '08.

[2]  K. Schulten,et al.  Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics. , 2003, Biophysical journal.

[3]  Klaus Schulten,et al.  Multilevel summation of electrostatic potentials using graphics processing units , 2009, Parallel Comput..

[4]  Carolina Cruz-Neira,et al.  VR Juggler: a virtual platform for virtual reality application development , 2001, Proceedings IEEE Virtual Reality 2001.

[5]  Klaus Schulten,et al.  Adapting a message-driven parallel application to GPU-accelerated clusters , 2008, 2008 SC - International Conference for High Performance Computing, Networking, Storage and Analysis.

[6]  Maxine D. Brown,et al.  The ImmersaDesk and Infinity Wall projection-based virtual reality displays , 1997, COMG.

[7]  Robert Drees.  Virtual Reality in Chemistry , 1997 .

[8]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[9]  Antoine Ferreira,et al.  Prototyping bio-nanorobots using molecular dynamics simulation and virtual reality , 2008, Microelectron. J..

[10]  Patricia J. Teller,et al.  Proceedings of the 2008 ACM/IEEE conference on Supercomputing , 2008, HiPC 2008.

[11]  Klaus Schulten,et al.  High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs , 2009, GPGPU-2.

[12]  Klaus Schulten,et al.  GPU acceleration of cutoff pair potentials for molecular modeling applications , 2008, CF '08.

[13]  Vladimir Pavlovic,et al.  Speech/Gesture Interface to a Visual-Computing Environment , 2000, IEEE Computer Graphics and Applications.

[14]  John E. Stone,et al.  Long time-scale simulations of in vivo diffusion using GPU hardware , 2009, 2009 IEEE International Symposium on Parallel & Distributed Processing.

[15]  Jan F. Prins,et al.  SMD: visual steering of molecular dynamics for protein design , 1996 .

[16]  Oliver Kreylos,et al.  Environment-Independent VR Development , 2008, ISVC.

[17]  John E. Stone,et al.  Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters , 2010, International Conference on Green Computing.

[18]  Carolina Cruz-Neira,et al.  Surround-Screen Projection-Based Virtual Reality: The Design and Implementation of the CAVE , 2023 .

[19]  Klaus Schulten,et al.  Accelerating Molecular Modeling Applications with GPU Computing , 2009 .

[20]  Josephine Anstey,et al.  Commodity-based projection VR , 2004, SIGGRAPH '04.

[21]  Michel F. Sanner,et al.  Role of haptics in teaching structural molecular biology , 2003, 11th Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems, 2003. HAPTICS 2003. Proceedings..

[22]  Robert van Liere,et al.  Experiencing 3D interactions in virtual reality and augmented reality , 2004, EUSAI '04.

[23]  Yoshifumi Kitamura,et al.  3D Interaction With and From Handheld Computers , 2004 .

[24]  Henry Sowizral,et al.  Embedding the 2D interaction metaphor in a real 3D virtual environment , 1995, Electronic Imaging.

[25]  John E. Stone,et al.  Probing Biomolecular Machines with Graphics Processors , 2009, ACM Queue.

[26]  Klaus Schulten,et al.  GPU-accelerated molecular modeling coming of age. , 2010, Journal of molecular graphics & modelling.

[27]  Russell M. Taylor,et al.  VRPN: a device-independent, network-transparent VR peripheral system , 2001, VRST '01.

[28]  Klaus Schulten,et al.  A system for interactive molecular dynamics simulation , 2001, I3D '01.

[29]  S. Lowen.  The Biophysical Journal , 1960, Nature.

[30]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[31]  Laxmikant V. Kale,et al.  MDScope - a visual computing environment for structural biology , 1995 .