Molecular Dynamics Showcase Builder

By Michael McLennan1; Nicholas K Kisseberth1; George A. Howlett1; Jim Slopsema1; Aleksei Aksimentiev2; Chen-Yu Li2

1. Purdue University 2. University of Illinois at Urbana-Champaign

Tool to create showcases for the Molecular Dynamics Showcase viewer.

Launch Tool

This tool version is unpublished and cannot be run. If you would like to have this version staged, you can put a request through HUB Support.

Archive Version 1.01
Published on 16 Nov 2015 All versions

doi:10.4231/D3FX74018 cite this

Open source: license | download

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Tools

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Abstract

This tool uses VMD as a visualization engine, but provides a simpler view of the interesting features within a molecular dynamics trajectory file. For each given dataset, users can choose from among a handful of scenes. Each scene has an associated trajectory with comments describing the view. Sections of the timeline may be further highlighted to explain the behavior within particular time ranges.

Use the various tools beneath the visualization to rotate, pan, zoom, or reset the view.  Use the ? tool to select atoms and measure distances and angles.  Use the "play" buttons to play forward or backward through the simulated frames, to view the system as a function of time.

You can download the data to your own desktop for further analysis.  We encourage you to cite any data that you use in academic publications by using the citation instructions provided under the button marked "Cite this work."

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VMD (Visual Molecular Dynamics) is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois at Urbana-Champaign. For more details, see http://www.ks.uiuc.edu/Research/vmd/

Sponsored by

Development of this visualization tool was supported by NSF 1227110, "Network for Computational Nanotechnology Cyber Platform" in conjunction with NSF 1227034, "Network for Computational Nanotechnology - NanoBIO Node."

Cite this work

Researchers should cite this work as follows:

  • Michael McLennan, Nicholas K Kisseberth, George A. Howlett, Jim Slopsema, Aleksei Aksimentiev, Chen-Yu Li (2016), "Molecular Dynamics Showcase Builder," https://nanohub.org/resources/mdshowbuilder. (DOI: 10.4231/D3FX74018).

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Tags

  1. Illinois
  2. molecular dynamics (MD)
  3. nano/bio
  4. NanoBio Node at Illinois
  5. NCN Group - Biotechnology and Medicine
  6. Visual Molecular Dynamics (VMD)