Visual Molecular Dynamics (VMD) is a very powerful program (available for Unix, MacOS X, and Windows) that allows users to visualize their MD data.

VMD allows users to create a .vmdrc file that is sourced the program’s start-up. This file should be located in your home directory (/home/username).

My .vmdrc file looks like:

display projection orthographic
menu main on
display nearclip set 0
axes location off
color Display Background white
display depthcue off
atomselect macro noh {not (mass 1.008 and charge < 0.25)}
set env(VMDFILECHOOSER) FLTK
color Labels Atoms black
color Labels Bonds black
label textthickness 2.0

The explanation:

  • The default projection is “perspective,” which will make things closer to the screen larger. Instead of a square box in orthographic, perspective is more of a triangular box shape.
  • Using menu main on ensures that you will have the main menu (which is important if you haven’t memorized the command prompt for every single thing VMD does) at all times.
  • Nearclip controls how distinctly and crisply items pop out of the screen; the most clean view is achieved at lower values.
  • The axes are turned off because they are relative and any generated images or movies shouldn’t include them.
  • The default background color is black. Any images or movies that are generated should be made with a white background.
  • Depthcueing is the front-to-back shading of loaded molecules. When depthcue is off, there is no shading/automatic transparency.
  • The default of VMD removes all hydrogens. By using the atomselect line, any polar hydrogen atoms are shown.
  • FLTK is an independent file chooser that should effectively be the default for most *nix systems. This line is especially important when using Mac OS, due to some issues with trying to use a Mac-based file chooser. The other choice for VMD is TK.
  • The default atom labels are green. Black is way easier to see on the white background.
  • The default bond labels are also green. Again, black on white is easier to read.
  • The default labels are thin and hard to read. This makes them bolder.