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Molecular Dynamics Showcase

By Michael McLennan1, Chen-Yu Li2, john stone3, Aleksei Aksimentiev2

1. Purdue University 2. University of Illinois at Urbana-Champaign 3. UIUC

View interesting features of a molecular dynamics trajectory file

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Version 1.0 - published on 08 Apr 2015

doi:10.4231/D3348GH3F cite this

Open source: license | download

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    Default example (opening screen) DNA diffusing through a nano pore Measure bond lengths and angles in PEG chain



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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

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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; Chen-Yu Li; john stone; Aleksei Aksimentiev (2015), "Molecular Dynamics Showcase," (DOI: 10.4231/D3348GH3F).

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Tags, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.