Visual Molecular Dynamics

Getting Started
Start VMD by typing:
vmd &

This should bring up the vmd GL DIsplay window (complete with rotating VMD logo), the main control window and the consol window. Let's start with the hardcore stuff and read in a pdb file. This lovely little number happens to be horse liver alcohol dehydrogenase with NADH.
  • In the Main window for vmd, click on the Mol button. A files subwindow will pop up.
VMD Main
    • In the files subwindow, select the format (in this case select pdb only).
    VMD File
    In addition:
    • Clicking on Select PDB button will bring up a File Selector Window, in which we can choose the proper file
    • Click in the directory area of the File Selector Window, change the working directory to /users/hurley/SciViz, and select 2ohx.pdb . Hitting return will bring you back to the Files subwindow.
    • Nothing is actually done by the program until you click on the Load Molecule button in the Files subwindow.
    Exercise 1
    Playing with the display:
    The Display button is NOT used to change how the molecule is drawn. The Graphics button is. We can do fun things like
    • Color by residue (ResName under Coloring Method)
    • Change the drawing method to ribbons
    • Change the drawing method to vander Waal's spheres change the drawing method to ball and stick (CPK)
    vmd graphics

    I wouldn't advise selecting Drawing Method : Off unless you have a REALLY good imagination. Try playing with the buttons for a few minutes before we go to a more manageable test case.

    NOTE: A lot of the windows are linked here and it's very possible to reach a certain window through several different paths (e.g. the Color window may be reached via the main menu or through the Color Defs button in the Graphical Representations window).

    NOTE: VMD can handle multiple molecules, so you can read in several at once and compare structures etc.

    Exercise 2
    Use Babel to convert the G94 output nadanal.log into pdb format. In a side window, type:
    babel-1.6/babel -ig94 nadanal.log -opdb nadanal.pdb
    • Read in nadanal.pdb in the same way as before. The molecule is rotated around various axes by depressing the left or middle mouse button.
    • Change the background color. This is done by opening the Color subwindow off the main menu and selecting Category:Display, Names:Background and selecting a color. 
    vmd color

    From here:

    • Change the background to white and convert the image to a postscript file through the Render subwindow (which is opened through the Render button on the main menu). Note that vmd will automatically open ghostview to display the postscript file.
    • Turn the background back to black.
    • Open the Display subwindow and make yourself see double by changing the Stereo control from Off to SideBySide
    vmd display
    Alanine Animation

    Another strength of VMD lies in its ability to playback trajectories resulting from molecular dynamics simulations. A sample trajectory, alanin.DCD is provided in the proteins directory of VMD versions 1.2b1 and larger. To load it, click on the Mol button of the button bar to bring up the Molecules form. Next click on the Load From Files button and select the psf and dcd option under the Molecule File Types listing. Select alanin.psf for the psf file and alanin.DCD for the DCD by clicking on the Select psf and Select dcd buttons respectively. After this, you need only click the Load Molecule button in order to begin reading the trajectory. In the display window you should see a simulation of an alanin residue in vacuo. It isn't particularly informative, but you can easily see that the structure is quite unstable in an isolated environment. After the DCD file has loaded, it will by default stop. To see it again or to fine- tune playback, open the Animate form by clicking on the appropriate button in the button bar. Press the button that looks like >> to play the animation. Use the slider at the bottom of the form to change the speed of playback. By rotating the molecule around, etc. you should get an idea about how the system destabilizes over the course of the simulation.

    David Johnson
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