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 old "cartoon" representation, where there are sometimes gaps between tubes and beta sheets. Use the "NewCartoon" representation which doesn't have these problems.
  • None of the external renderers support 3-D texturing "color by volume" yet.
  • The Tachyon and LibTachyon renderers sometimes render an incorrect image when several user-defined clipping planes are activated simultaneously.

MacOS X Specific

  • 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 a problem with the Tk toolkit, that code isn't part of VMD itself.
  • Currently shipping versions of MacOS X (10.3.x) have OpenGL drivers that don't display VMD's "color by volume" 3-D texture maps correctly. We are currently working with Apple to solve this problem, with a MacOS X update, or by changing VMD if necessary.
  • 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 MacOS X version of STRIDE fails to compute the secondary structure for the system "1S5L" with the selection "protein".

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.
  • The 64-bit SGI IRIX version of VMD 1.8.3 includes a 'psfgen' plugin that crashes when used. We are working on a resolution to this problem.
  • ATI's fglrx 8.10.19 Linux drivers crash immediately when creating the main VMD OpenGL window. Use a newer or older driver release.

Windows Specific

  • The 'vmdmovie' plugin has problems compressing movies into directories with names containing spaces, due to issues with the "VideoMach" program.