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Supported Applications

VMD

  • Description

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

  • Usage 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.

  • Primary Citation*

    W. Humphrey, A. Dalke, and K. Schulten. 1996. VMD - Visual Molecular Dynamics. Journal of Molecular Graphics. 14: 33-38.


    • *Full citation information available through

  • Citation Note

    The authors request that all published work which utilizes VMD include the primary VMD citation at a minimum.

  • Tales

    Computing Cellular Clockworks

    Computing Cellular Clockworks

    Physicist Klaus Schulten once imagined becoming a dancer, relying on nothing but his own mind and body to perform. “But I was not a good dancer,” he says. “So my next thing was theoretical physicist. Just myself, pencil and paper — and in my case, also an eraser.”

    That dream was also thwarted. Today, Schulten relies on some of the most powerful and expensive computing equipment on earth to carry out his work, which applies theoretical physics to the understanding of biological systems. His most recent work involved the molecular simulation of an organelle that converts light energy to chemical energy inside a photosynthetic bacterium using the molecular dynamics tools NAMD and VMD, which his lab develops. Looking forward, he wants to simulate an entire living cell, right down ...

    Read More.
  • Webinars

    Topic: xMDFF, a new molecular dynamics flexible fitting-based approach.
    Presenter: Abhishek Singharoy, Postdoctoral Fellow, Beckman Institute and University of Illinois at Urbana Champaign.

    Host: Jason Key
    Recorded on December 6, 2016

  • Categories

    Structure Visualization & Analysis

  • Default Versions

    Linux 64:  1.9.3
    OS X INTEL:  1.9.3

  • Other Available Versions

      Linux 32:

      1.9.1, 1.9, 1.8.7
    • Linux 64:

      1.9.2, 1.8.7
    • OS X INTEL:

      1.9.2, 1.8.7
    • powermac:

      1.8.7, 1.8.6, 1.8.5
  • Developers

    Klaus Schulten, John Stone, VMD Developer Team.

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