With my new quad-core I decided to install [email protected] on my Ubuntu Karmic. It is very easy using the origami installer. I just ran the following to install with team Ubuntu as my team:

sudo apt-get install origami && sudo origami install -t 45104 -u USERNAME

Unfortunately, while it is niced by default, it keeps the CPU running at 100%. This means the CPU uses more electricity and runs hotter. Most annoyingly, IMHO, it also keeps the fan at full speed meaning additional noise.

My solution was to change the ignore_nice_load setting of the ondemand frequency governor from 0 to 1. In Ubuntu Karmic I had to do it by editing the special boot script in /etc/init.d/ondemand. This script changes the frequency governor from performance to ondemand after the system has booted. I simply added the following to line 29:

echo -n 1 > /sys/devices/system/cpu/cpu0/cpufreq/ondemand/ignore_nice_load

In a multi-core setup the value seems to propagate to other cores automagically. Now my processor scales back to the minimum 800 MHz while idle, but uses any excess power to fold proteins in the grid.

Update:
I found that 800 MHz isn't fast enough to complete the work units in time for their deadlines (my computer isn't on 24/7). I switched to gravitational waves and QMC using the BOINC client instead. It's a bit more of a hassle to set up, but seems to be running fine.