Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories

John E. Stone, Kirby L. Vandivort, Klaus J Schulten

Research output: Contribution to journalConference articlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1-12
Number of pages12
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6939 LNCS
Issue numberPART 2
StatePublished - Oct 5 2011
Event7th International Symposium on Visual Computing, ISVC 2011 - Las Vegas, NV, United States
Duration: Sep 26 2011Sep 28 2011

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)


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