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Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis
Published on: December 18, 2014
Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for
Rudesh D Toofanny1, Andrew M Simms, David A C Beck
1Department of Bioengineering, University of Washington, Seattle, Washington 98195-5013, USA.
BMC Bioinformatics
|August 12, 2011
Summary
Spatial indexing significantly speeds up atomic contact calculations in molecular dynamics (MD) simulations. This method enhances data analysis and reduces computational time for large-scale simulations, improving scientific discovery.
Area of Science:
- Computational biology
- Biophysics
- Data science
Background:
- Molecular dynamics (MD) simulations provide insights into macromolecular dynamics and atomic interactions.
- Calculating atomic contacts from MD trajectories is computationally intensive, scaling exponentially with system size.
- Spatial indexing (spatial hashing) divides simulation space into bins for efficient contact discovery.
Purpose of the Study:
- Implement and evaluate a spatial indexing algorithm for accelerating atomic contact calculations in large MD simulation databases.
- Assess the impact of data compression techniques on performance and storage for MD trajectory data.
Main Methods:
- Implemented a spatial indexing algorithm within a multi-terabyte MD simulation database.
- Applied the algorithm to data from the Dynameomics project.
- Tested data and index compression using MS SQL SERVER 2008 options on trajectory coordinate tables.
Main Results:
- Spatial indexing accelerated contact calculations by 1.2-10.3 times (14-90% speedup) for 1 ns windows.
- For a 51 ns trajectory, spatial indexing provided 1.4-5.3 times faster calculations (31-81% reduction in runtime).
- Page level compression reduced table sizes by ~36% with no significant impact on execution time.
Conclusions:
- Spatial indexing substantially decreases the time required for atomic contact calculations, applicable to other neighbor discovery problems.
- The speedup facilitates on-the-fly analysis and visualization, enabling rapid knowledge discovery.
- Page compression offers significant disk space savings (~36%) for non-transactional MS SQL SERVER 2008 databases without performance degradation.
