From: Benjamin Bouvier (
Date: Fri Jun 12 2009 - 10:45:37 CDT


Here is the log. It appears to be more related to the Linux machine
actually running VMD than to the Macbook doing the displaying, though...

Info) VMD for LINUXAMD64, version 1.8.7beta5 (June 1, 2009)
Info) Email questions and bug reports to
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 7302MB (94%)
Info) No CUDA accelerator devices available.
Info) ATI Linux driver detected, limiting features to avoid driver bugs.
Info) Set the environment variable VMDDISABLEATILINUXWORKAROUND
Info) to enable full functionality on a known-safe driver version.
Info) OpenGL renderer: ATI Radeon X1600 OpenGL Engine
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (4096x4096), Multitexture (8)
vmd >

On Fri, 12 Jun 2009 17:36:49 +0200, John Stone <> wrote:

> Benjamin,
> If you run one of the recent VMD 1.8.7 beta versions, the console
> output will occur in whatever terminal you started VMD from. So this
> would be on your original ssh/xterm session, etc. Check there.
> Cheers,
> John
> On Fri, Jun 12, 2009 at 05:28:17PM +0200, Benjamin Bouvier wrote:
>> Hi John,
>> When I tried to find the VMD console to check the startup log, I was
>> unable to find it, though it is listed as opened by the X11 server. It
>> seems that *somehow* the console opens inside the OpenGL window, hence
>> the
>> flashing -- what I had described as white frames in my previous posts
>> seem
>> in fact to contain garbled text (it varies upon dragging the window
>> around), which is reminiscent of the console window...
>> Is there a startup switch to log the console output to some file? If
>> so, I
>> could retrieve the startup message there. I looked quickly in the manual
>> but could not find one...
>> Cheers,
>> Benjamin
>> On Fri, 12 Jun 2009 17:02:33 +0200, John Stone <>
>> wrote:
>> >
>> >Benjamin,
>> > Can you send me the VMD startup messages you get when you
>> >display on the remote machine? The description you're giving
>> >sounds like they've somehow created a new bug/problem with
>> >OpenGL double buffering. I don't recall if glxgears is using
>> >double buffering or not, so the lack of trouble there may
>> >not be indicative of anything. If you send me the VMD startup
>> >messages, it will tell me more about what features their X11
>> >server implementation is advertising to the client Linux system,
>> >and with this we may be able to narrow down the source of the problem.
>> >
>> >CHeers,
>> > John Stone
>> >
>> >
>> >On Fri, Jun 12, 2009 at 04:48:29PM +0200, Benjamin Bouvier wrote:
>> >>Hi all,
>> >>
>> >>I usually run VMD on a remote Linux machine (cluster frontend) and use
>> >>MacOs's X11 implementation to forward the display to my MacBook Pro.
>> >>This
>> >>used to work fine.
>> >>
>> >>No so since I upgraded MacOS from 10.5.6 to the latest 10.5.7. The
>> >>contents of the VMD OpenGL window flash very quickly (one frame is
>> >>white,
>> >>the second one is the actual VMD rendering), making VMD unusable. This
>> >>occurs with VMD 1.8.6 and 1.8.7, both 32 and 64 bits.
>> >>
>> >>I read that Apple had done modifications to X11 in 10.5.7. However,
>> the
>> >>problem seems limited to VMD : glxgears for instance is forwarded OK,
>> as
>> >>are all non-openGL windows (including the VMD Main window).
>> >>
>> >>Are there any other users experiencing this ? Is there a simple cure ?
>> >>
>> >>Thanks,
>> >>--
>> >>Benjamin Bouvier
>> >

Benjamin Bouvier
Structural Bioinformatics
IBCP Lyon - UMR 5086 CNRS
7, passage du Vercors
Tel: +33(0)4-37-65-29-44