A system for interactive molecular dynamics simulation
I3D '01 Proceedings of the 2001 symposium on Interactive 3D graphics
Visualization of particle traces in virtual environments
VRST '01 Proceedings of the ACM symposium on Virtual reality software and technology
Efficient view-dependent out-of-core rendering of large-scale and complex scenes
Proceedings of the 2006 ACM international conference on Virtual reality continuum and its applications
Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization
IEEE Transactions on Visualization and Computer Graphics
Immersive Visualization and Analysis of LiDAR Data
ISVC '08 Proceedings of the 4th International Symposium on Advances in Visual Computing
Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units
Interactive Visualization of Molecular Surface Dynamics
IEEE Transactions on Visualization and Computer Graphics
Immersive molecular visualization and interactive modeling with commodity hardware
ISVC'10 Proceedings of the 6th international conference on Advances in visual computing - Volume Part II
Coherent culling and shading for large molecular dynamics visualization
EuroVis'10 Proceedings of the 12th Eurographics / IEEE - VGTC conference on Visualization
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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.