Joe Presswood,
The answer to the best optimization of your HP Z820 for fluid / gas simulation is more complex than formerly as more applications are using GPU acceleration. This kind of simulation is CPU based, and formerly I'd suggest simply to add the 2nd CPU, but today there is the amazing option to add a GPU coprocessing unit. Formerly, you needed to be using NAMD (molecular biology, protein folding etc) or whether simulation applications, writing custom C++ code to use it, but today the list of GPU-accelerated software is becoming mainstream and Autodesk and Adobe plus many others can utilize NVIDIA CUDA-based co-processing units>
http://www.nvidia.com/object/gpu-accelerated-applications.html
> If your applications are on this list, I'd suggest looking into an NVIDIA Tesla GPU unit. The great feature of these is that no one knows what to do with them, so the previous models can be amazingly inexpensive >
http://www.ebay.com/itm/IBM-NVIDIA-TESLA-M1060-VIDEO-CARD-4GB-PCI-E-X16-VIDEO-CARD-43V5909-/190842360798?pt=PCC_Video_TV_Cards&hash=item2c6f1753de
> an eBay listing for someone with 10 Tesla M1060 4GB coprocessors- new $2,200, but today "Buy It Now" for $85! For comparison, the current 6GB Tesla K20 costs, $3,300 and the K20X, (18,688 of which were used in the "Titan" supercomputer) is $7,500. This is not to say you can use these to advantage- or at all, but obviously if so, buy as many as you have slots for. There is also the Tesla C1060, C2050, C2070, C2075, and K20 to consider. The K20 is fantastically capable- for the right software, new is $3,400 and used is still $1,200- not impossible in your budget.
Given the processor emphasis of your use, it makes sense too to add the second CPU used for about $800-900. That is an extremely good CPU too > no. 10 on the Passmark CPU benchmark list- out of about 1,700 CPU's. ( About $1,300 new.)
The Quadro K2000 is a very good graphics card for your use, if in combination with something like the M1060. If so, add as many as you have slots, add the second E5-2660, upgrade RAM to 32GB. Remember to buy a matching second fan and/or heatsink for the second CPU. I would have no qualms about buying a Xeon used, and an E5-2660 today costs about $850-900.
Another strategy would be to buy a used K20 ($1,200)or C2050 /2075, and a second, used E5-2660 ($900 with second heatsink), +8 GB RAM to make 32GB ($75).
If you're not able to use GPU co-processing, for your $2,000, you might buy a used K5000 (about $1,300) which will act as a GPU accelerator, used E5-2660 ($900), and if your file size can be large, perhaps upgrade to 32GB RAM. -a bit over your budget,.. You don't mention ECC, but with particle / gas simulation, the error correcting can be your friend- certainly not faster, but more accurate.
One component not mentioned is the monitor, and in my view, a very useful upgrade wold be to consider- it you don't have it, adding a 27'" 2560 X 1440 monitor for the image window and running a second monitor for menus and viewports.
Cheers,
BambiBoom
[Dell Precision T5400 > 2X Xeon x5460 quad core @ 3.16GHz, 16GB ECC, Quadro FX 4800 (1.5GB), WD RE4/ Segt 500GB] [Windows 7 Ultimate > AutoCad, Revit, Solidworks, Sketchup, Adobe CS, Corel Technical Designer, WP Office, MS Office] [ Monitor> HP 2711x / 27" 1920 X 1080)