[Freakin]

I'd probably go with server hardware and get a high quality motherboard that can take 8-16GB of FB memory.

Raid 1 is probably a good idea also, since I'm guessing losing all your data would be bad. Raid 1 means it's constantly writing the same data to both harddrives so if one fails you don't lose any data. This does not replace the necessity of backups, however.

The most important thing to figure out directly from the programmer is whether or not it is multithreaded, like nuclear500 said.

Multithreaded means that there are different 'parts' of the program that can be assigned to multiple processors. If it's not multithreaded, you need the best 'core' of a processor you can afford; you won't benefit from dual-core, quad-core, or dual processors unless you are running your simulation many times at once.

If it IS multithreaded, then you should look at good multi-core systems.

Personally I would try to get quad-core xeons on a server board, and probably get 2 10k or 15k RPM SAS drives in Raid 1. A good raid controller is also probably important.