Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories

  • John E. Stone
  • Kirby L. Vandivort
  • Klaus Schulten
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6939)

Abstract

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.

Keywords

Molecular Dynamic Trajectory Trajectory Data Trajectory Format Atomistic Molecular Dynamic Molecular Visualization 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • John E. Stone
    • 1
  • Kirby L. Vandivort
    • 1
  • Klaus Schulten
    • 1
    • 2
  1. 1.Beckman Institute for Advanced Science and TechnologyUniversity of IllinoisUrbana-ChampaignUSA
  2. 2.Department of PhysicsUniversity of IllinoisUrbana-ChampaignUSA

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