ccperf721p has put up a How To for Quad core folding on Linux. It is worth a look if this is your cup of tea.

Posted by ccperf721p:

This is a 64 bit Linux How To, it will not work with VMware..
After running folding@home's SMP client on several dualcores then moving into a quad I noticed that it does not perform as expected, giving only a 33% gain in performance. After scouring the net it seems the best solution is to run dual smp clients and setting affinity to 2 cores for each client.

Read the "HOW TO" here