John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
Immersive out-of-core visualization of large-size and long-timescale
molecular dynamics trajectories.
Lecture Notes in Computer Science, 6939:1-12, 2011.
(PMC: 3032211)
STON2011B
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 longtimescale 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.
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