I started with Unix on a Personal IRIS as an undergrad working in a physics lab which used it for imaging capture and analysis. I was the nominal sys admin, with one semester of Minix under my belt and just enough to be dangerous. (I once removed /bin/cc because I thought it was possible to undelete, like on DOS. I had to ask around the meteorology department for a restore tape.)
The summer before grad school I got a job at the local supercomputing center to work on a parallelization of CHARMm, using PVM. I developed it on that PI, and on a NeXT. That's also when I learned about people at my future grad school working on VR for molecular visualization, in a 1992 CACM article. So when I started looking for an advisor, that's the lab I chose, and I became the junior co-author and eventual lead developer of VMD.
With a Crimson as my desktop machine, a lab full of SGIs and NeXTs, and the CAVE VR setup elsewhere in the building. Heady times.
I visited SGI in 1995 or so, on holiday, thinking that would be a great place to work. They even had an Inventor plugin for molecular visualization, so I thought it would be a good lead. I emailed and got an invited to visit, where the host kindly told me that they were not going to do more in molecular visualization because they wanted to provide the hardware everyone uses, and not compete in that software space.
In the early 1990s SGIs dominated molecular modeling (replacing Evans & Sutherland), so naturally the related tools, like molecular dynamics codes, also ran on them. But we started migrating to distributed computing, where it didn't make sense to have 16 expensive SGIs, leaving them more as the head .. which as you pointed out, was soon able to run just fine on a Linux machine.