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Doblack BN, Allis T, Dávila LP. Novel 3D/VR interactive environment for MD simulations, visualization and analysis. J Vis Exp. 2014;(94)doi: 10.3791/51384.
Doblack, B. N., Allis, T., & Dávila, L. P. (2014). Novel 3D/VR interactive environment for MD simulations, visualization and analysis. Journal of visualized experiments : JoVE, (94), . https://doi.org/10.3791/51384
Doblack, Benjamin N, et al. "Novel 3D/VR interactive environment for MD simulations, visualization and analysis." Journal of visualized experiments : JoVE vol. ,94 (2014). doi: https://doi.org/10.3791/51384
Doblack BN, Allis T, Dávila LP. Novel 3D/VR interactive environment for MD simulations, visualization and analysis. J Vis Exp. 2014 Dec 18;(94). doi: 10.3791/51384. PMID: 25549300; PMCID: PMC4396941.
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J Vis Exp. 2014 Dec 18;(94). doi: 10.3791/51384.

Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

Journal of visualized experiments : JoVE

Benjamin N Doblack, Tim Allis, Lilian P Dávila

Affiliations

  1. Materials Science and Engineering, School of Engineering, University of California Merced.
  2. Materials Science and Engineering, School of Engineering, University of California Merced; [email protected].

PMID: 25549300 PMCID: PMC4396941 DOI: 10.3791/51384

Abstract

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

References

  1. Phys Rev Lett. 2003 Nov 14;91(20):205501 - PubMed
  2. J Vis Exp. 2014 Nov 12;(93):e51372 - PubMed

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