You will have trouble doing Molecular Modeling on that system for now.
There are numerous issues with this drive and AGP support.
You will have to add in line in you XF86Config file so that it loads the right AGP support driver and it will not do AGP8X. That's what I have on a machine here and lets just say that my Quadro 2000 has given me nothing remotely close to what I was expecting.
I have a dual opteron and the Quadro 2000 and my PIII450 with a geforce2 at home gives me better 3d performance than the system here...
But anyhow. Here is the line you will need to add.
In the Device section, where you have "Driver "nvidia""
Option "NvAgp" "2"
You can change the value. I can't remember exactly but I know different values load different AGP options.
2 is the only one that works on my system.
PS: what are you using to do the Molecular rendering? I need to shop for one that will run on Linux whenever I can this system working better.