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.
  • The Postscript renderer export option skips spherical geometry in reps such as VDW, CPK, etc as a result of a missing routine for handling DSPHEREARRAY display commands.
  • The Windows version of the PSF plugin crashes VMD when running on Windows 2000 systems (but not on NT systems) for some reason.
  • The Cartoon representation fails to invoke Stride on some Windows 98 machines.
  • The File->Save State feature fails to save the config file correctly when any loaded molecule files have pathnames containing spaces.
  • The File->Save State feature fails to save the config file to directories containing spaces in their pathname.
  • The AIX 4 version of VMD terminates unexpectedly when the Graphics->Display Settings menu is accessed on some machines.
  • 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 appears to be some sort of FLTK problem and may already be fixed in FLTK 1.1.2 since that version didn't seem to behave this way. The workaround is to move the window initially.

MacOS X Specific

  • The VMD help button generates an error on older MacOS 10.1.x systems as the "/usr/bin/open" command on older revs of OS X don't permit URL's to be specified. This feature works fine with MacOS 10.2 or newer.
  • 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.
  • The Mac version doesn't use dynamically loaded VMD plugins yet
  • The Mac version doesn't support script-based Tk windowing yet.

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

  • Some Windows ME systems fail to work correctly with the Winzip self-extracting software installer code. Unzipping manually works perfectly.