From: Janet Jacobsen (
Date: Mon Sep 08 2008 - 18:46:07 CDT

Hi. I was asked to upgrade VMD from 1.8.3 to 1.8.6 on
a multi-user system for which I do not have root access.
It's a Linux x86_64 system (kernel 2.6.5).

I'll skip the details, but I went down the path of building
fltk, netcdf, the VMD plugins, and VMD with a version of
gcc that is consistent with the version of GL on the machine.

I cannot run vmd using the vmd script in ~bin (when I load
a molecule all windows disappear), but with the version I built,
I am able to run vmd by executing the binary in ~lib/vmd.

I have run through the tutorial and tried loading a few proteins,
and most of that seems to work, but the Extensions menu is

When I fire up VMD 1.8.3, I see a lot of entries in the Extensions
menu, so I assume that I should see the same extensions when
I start VMD 1.8.6. Any idea what step I may have missed in
building VMD? (As I mentioned above, I did compile the VMD
plugins, and I did define PLUGINDIR before compiling VMD.)

In general, I am confused about the difference between extensions
and plugins. I tried experimenting with the .vmdrc file and with
"package require" at the command line, but based on my
understanding of the plugin documentation, I shouldn't need to
add plugins that come with the VMD distribution.

I'd appreciate any pointers you can give me.