Alas, there are still bugs and inconsistancies in VMD. Following is a list of known problems, limitations, and workarounds.


  • An incorrect PDB accession code or download failure causes a 0 atom molecule to be loaded, though error messages are printed to indicate the problem. Delete the extra molecule.
  • VMD contains a bug in the "cartoon" representation, where there are sometimes gaps between tubes and beta sheets. These will be fixed in a future version of VMD.
  • Changing some of the atom information (secondary structure classification, beta and occupancy values, etc.) doesn't update the graphics display automatically. Workaround: press the "Apply Changes" button on the graphics form.
  • The main VMD window will sometimes not respond to mouse clicks until the first time it is moved. This is some sort of FLTK problem, and will be fixed when future versions of VMD use newer FLTK code.

MacOS X Specific

  • Recent updates to MacOS 10.2 on machines with Radeon 9x00 series graphics boards have an OpenGL performance issue with VMD when the Axes are displayed. Disabling the Axes display with the Display--Axes--Off menu item will restore VMD rendering performance to the level one would expect on such hardware. We are looking into this problem and hope to have a solution for VMD 1.8.2.
  • The Mac version of VMD 1.8.1 isn't runnable by any user except for the one that originally installed it by default. This can be fixed by running the command below on your installed directory, replacing filenames with the appropriate path of course:
     chmod a+x "VMD" 
  • It is possible to crash VMD by using the cut/copy/paste functions on the top menubar when nothing is selected, this seems to be an issue with Tk/FLTK since that code isn't part of VMD itself.
  • The Mac version of MSMS appears to misbehave when generating a surface for some molecular structures. Specifically, loading the PDB '1hzx' does not produce a surface on the Mac, though it works fine on other platforms.

Unix Specific

  • Some SGI systems will return a stereo visual that only works with "above/below" stereo, which is not supported by VMD. In this case, VMD will incorrectly report that stereo is available, though it isn't really available.

Windows Specific

  • The Cartoon representation fails to invoke Stride on some Windows 98 machines.