From: Axel Kohlmeyer (
Date: Wed May 13 2009 - 17:45:44 CDT

On Wed, 2009-05-13 at 16:17 -0500, John Stone wrote:
> Hi,
> What GPU chipset/card do you have in your machine? It sounds
> to me like you have a video driver problem (flickering colors etc).

there also is the issue that ubuntu be default seems to have
visual effects via "compiz" enabled. i'm sitting in front of
a ubuntu 8.10 machine where this is the case and i had to
disable it to avoid lockups with CUDA codes while running VMD.


i guess a recommendation to be added to the linux release notes
would be (on Gnome desktops) to go to
click on the "Visual Effects" tab
and turn them off.


> Regarding LAMMPS, you're likely to want to try the updated LAMMPS
> plugin that's included in the new VMD 1.8.7 beta 2 version I just
> posted, as Axel Kohlmeyer just made several significant improvements
> to it.
> Cheers,
> John Stone
> On Wed, May 13, 2009 at 02:55:31PM -0400, wrote:
> > Hello,
> >
> > I just installed VMD(1.8.6 compiled from source code) on my linux machine (running ubuntu 9.04) and all went well during the installation but when I start the application the red green and blue colors of the spinning VMD letters and the coordinate axes keep flickering back and forth between white and the colors theyre supposed to be. I thought this odd but still went on to try and use the program to do a simmulation but everytime I load in a structure generated by LAMMPS code no picture shows up and there are zero time steps even though it recognizes how many atoms there should be and the time steps are specified. I have already ran the same simulation succesfully on a different machine and I have all the latest openGL, tcltk, and fltk libraries. What should I do?
> >
> > -Cody Knowles

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.