VMD (Visual Molecular Dynamics)

• VMD is a molecular visualization program for displaying, animating and analyzing large biomolecular systems using 3D graphics and built-in scripting
  • Freely available (requires registration) for Linux, MacOS & Windows
• Developed by Theoretical & Computational Biophysics Group at the University of Illinois
• https://www.ks.uiuc.edu/Research/vmd/
• This will be a very brief intro, more tutorials available at http://www.ks.uiuc.edu/Training/Tutorials/

High-quality rendering using the Tachyon ray tracer

Type-along: Starting VMD

• Assuming you’ve already installed VMD, click the VMD icon (Windows, MacOS) or launch vmd from the terminal (Linux)
  • On Dogmi workstations you need to add VMD to your $PATH:

  $ export PATH=/home/cscuser/vmd/bin:$PATH
  $ vmd

  • Now you can launch vmd without typing the full path to the binary

Tweaking the startup configuration

• Colors and appearance can be adjusted under “Graphics” and “Display”
  • White background typically nicer for publications, remove axes
• Configuration can be saved into a startup file .vmdrc
  • “Extensions” > “VMD Preferences”
  • Loaded upon startup (searched in current, home and install directories)

Example 1: Small protein in water

• VMD supports tens of different file formats
• Download a small protein structure file (wget or open URL in browser)

$ wget https://a3s.fi/CSC_training/protein.gro

• Open in VMD: “File” > “New Molecule” > “Browse” > “Load”
• Rotate the molecule:
  • Left click for free rotation, right click around viewing axis
  • Other possibilities (translate/scale): “Mouse”
  • Reset view with “=”
• Atoms and bonds can be also be measured, moved and deleted
  • Deleting bonds might be handy if bonds stretch across PBC

Representations 1

Representations 2

• Try creating three representations, one with selection “protein” (or “not solvent”), one with “solvent and within 10 of protein”, and one with “ions”
  • “Create Rep”, type in “Selected Atoms”
• Play with different draw styles, e.g.:
  • Protein: “Secondary Structure”, “Opaque”, “NewCartoon” (change “Display” > “Rendermode” > “Acrobat3D” if buggy)
  • Solvent: “Element”, “Transparent”, “QuickSurf” (try different resolutions)
  • Ions: “ColorID 7”, “Opaque”, “VDW”

Custom materials

Rendering high-quality images 1

• Now let’s render a nice picture of our system
  • Add another representation for the protein using the previous custom material
  • For clarity, lets toggle off the solvent
• Go to “File" > ”Render"
  • Render using the Tachyon engine (select from dropdown menu)
  • Add -res 1000 1000 to “Render Command” to increase resolution to 1000x1000 px
  • Press “Start Rendering”

Rendering high-quality images 2

We got a nice picture, but can we make it even better?

• Go to “Display” > “Display Settings” and toggle on “Shadows” and "Amb. Occl." under “Ray Tracing Options”
• Change ions and protein materials to “AOShiny” for a material with good AO compatibility
• Render the view as previously (this will now take a bit longer, decrease resolution for faster results)
• Convert output to .png or .jpg if needed (use e.g. convert on Linux):

$ convert vmdscene.dat.tga protein.png

Example 2: Ruthenium bipyridyl complex on a TiO₂ surface

• VMD can be used to visualize .cube files as well (e.g. densities, orbitals)
• Let’s visualize bond-induced electron density differences of a ruthenium bipyridyl complex on a TiO₂ surface
• Go to https://a3s.fi/CSC_training/surface.cube or download the structure with wget

$ wget https://a3s.fi/CSC_training/surface.cube

• Open the file in VMD

Representations 3

• Create separate representations for the surface and the adsorbed complex
  • Try selections “z < 20” and “z > 20”
  • CPK is a good option for the drawing style
• Create two more representations with selection “all”
  • Use “Isosurface” drawing method with settings:
    • Isovalue: -0.003 and 0.003 with ColorIDs 0 (blue) and 1 (red)
    • Draw: Wireframe
    • Show: Isosurface
• Explore the structure, where can you see increase/decrease in electron density?

Rendering high-quality images 3

• Change “Wireframe” to “Solid Surface” and the material of the isosurfaces to the custom material created in the previous example
• Turn on shadows and ambient occlusion lighting under “Display Settings” and render the view as previously
  • Again, this might take a while, decrease resolution for faster results

Your turn!

• Continue playing around with the lysozyme or ruthenium bipyridyl structures
• Or try something else (download with wget or browser):

$ wget https://a3s.fi/CSC_training/pcbm.xyz  # PCBM molecule
$ wget https://a3s.fi/CSC_training/dna.pdb  # DNA dodecamer

• You can also use any other structures of your own
• Ask for guidance and tips!
  • Tutorials available at http://www.ks.uiuc.edu/Training/Tutorials/

What next?

• Animations and movies
• Analyses and extensions
• Scripting

Thanks for your attention!