VMD

  • a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Developers

VMD Developer Team

Categories

Structure Visualization

Versions

Citations

Humphrey et al. VMD - Visual Molecular Dynamics. J. Molec. Graphics. 1996. 14: 33-38. For a list of other citations go to: http://www.ks.uiuc.edu/Research/vmd/allversions/citations/

Technical Notes

Condensed “movie making tips” from VMD. The main points:

  1. Just load 1 frame for every 1ns of simulation time. A 1 us simulation would only need 1000 frames. The “stride” feature in the VMD trajectory loader dialog lets you set this (e.g. to 20, if the generated frames are at a rate of 50 ps per frame). Make sure you choose “load all frames at once”, rather than “background”. The “background” option will render frames as they’re loaded.

  2. Figure out what region you want to “fix” in the structure. Get the residue IDs for this. Go to Extensions→Analysis→RMSD Tool and enter “protein and resid START to STOP”, then click on “Align”. This will align the entire structure through all frames and have resids START to STOP as stationary as possible.

  3. Use “Create Rep” to create multiple representations of the structure. The selection box can be used to specify what you want to show. “protein and resid START1 to STOP1 START2 to STOP2 …” is a common entry. “water and within 3 of protein” would show all water molecules within 3A of an atom associated with a protein. You can then play with the different kinds of views (coloring, style, transparency) for each representation individually.

  4. Clicking on a representation will show or hide it.

  5. For each representation, set the Trajectory to smooth over several frames. I have found that a 4ns smoothing window reduces the jitter without eliminating interesting side chain motion. YMMV.

  6. Set Display→Rendermode→GLSL to do OpenGL/CUDA rendering. This should make a big difference. I haven't done a formal test of this, but my laptop, with 48 CUDA 3 processing cores, seems to do much better, smoother, and faster rendering than my Mac Pro (which does not have a compatible CUDA card).

Movie Making:

  • loaded every 20th frame (about 1000 from 20k) * smoothing window of 4 * internal Tachyon ray tracer * image smoothing on * half size reduction * 30 FPS (NTSC) * MPEG output

Apparently a good trick to get nice looking animations is to double the rendering window then set the movie generator to half-size the result. I guess this gives a “per-frame” image smoothing effect as the potentially hard edged rendered image is reduced to an anti-aliased frame.

License Type

This software is distributed under a Non-Profit license.

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