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VMD_tutorial.md

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How to use VMD

Installing VMD

The pre-compiled version of the software can be downloaded here (for both LINUX and MacOS X). Registration (harmless) is required.
Then the instructions at this link can be followed to install it.

Visualization of MD trajectories

  1. The VMD Main and OpenGL Display panels: going through a loaded trajectory, rotate, translate, zoom in/out and reset view
  2. The Graphical Representations panel: changing the visual representation of the molecules, making selections, visualization of multiple frames

Comparing different trajectories from SimpleMD

  1. Opening multiple trajectories at the same time
  2. Wrapped atoms inside the box
  3. Comparing the system behavior under different conditions: no forces, with forces, melting
  4. Save visualization state
  5. Rendering nice images from VMD visualization

A more biological example: visualizing GAC RNA

  1. More specific selections: nucleic, water, ions, resid
  2. Playing with the graphical representations