3 pin fan control explanation.

3-pin fans have a positive pin (where the fan gets power from), ground pin (negative pin), and tachometer pin (tells you how fast it's turning).

The idea is that the fan runs at full speed when you have 12 volts on the positive pin, but if you apply 7 volts to the pin instead, the fan turns slower. If you lower the voltage enough, the fan will eventually stop. This normally occurs around 4-6 volts. All of this occurs on the positive pin.

This is about the extent of how most people think of voltage control, but there's an entire world of confusion when you start talking about HOW the controller goes from 12 volts to 7 volts. This is very important when you start talking about water pumps or magnetic bearings (Corsair ML Pro fans).

If I've answered your question at this point, you can ignore what follows. It gets pretty hairy.

In order to control the voltage that the fan is running at, the controller does not actually generate a 7 volt signal. It actually can't, as that requires some really expensive parts. Instead, it turns the power to the fan on and off very quickly. It uses the ratio between on and off (called duty cycle) to vary the amount of power that the fan gets. This is called PWM, and it is used on the power pin of the 3-pin fan when you set it up to be "voltage controlled". Confused yet? So was I. It turns out that the only difference between 3-pin and 4-pin fans is that in the 3-pin fan, the PWM signal is combined with the power signal, and it is separated to the 4th pin of a 4-pin fan. A 4-pin fan must recombine the PWM control signal back into the power signal in order for speed control to work. The advantage of the 4-pin design is that the fan's control circuits can still have power even when the motor is in "off" mode from the PWM signal.

There are many reasons that they treat 3 and 4 pin fans differently. For example, for magnetic bearings, you need power for the bearing at all times. Turning the power to the fan on and off (3-pin) would also turn the bearing on and off. That's bad. In a 4-pin setup, though, the PWM signal is separate from the power, allowing the bearing to stay on even as the motor switches on and off.

Another advantage of the 4-pin approach is that you have power for the fan's circuitry at all times. In the 3-pin setup, the fan's circuits effectively have to "reboot" each time you turn them back on. This means that in the 4-pin design, you can switch everything at a frequency that people can't hear. In a 3-pin design, you have to switch at a much lower frequency and often generate audible noise as a result.

Sorry if that was confusing, but this entire subject is rather complicated. There are many more details that play into how speed control works, but I tried to limit this post to the parts that are important for most people.

Oh, you meant to ask how to use it, not how it works?

In that case, you simply go into BIOS, select "Hardware Monitor" on the middle of the right hand side, and in the second to the bottom pane, select the fan you want to control, and use the sliders to set the target temperature, min and max fan speed.

Your motherboard only seems to support one temperature sensor (the CPU), so it cannot account for GPU heat this way.

Irrespective of the details of how the voltage is adjusted (the latter part of the stuff above), a 3-pin fan IS controlled by the mobo header using software in the BIOS. That is, IF the header is using Voltage Control Mode (aka DC Mode).

The voltage supplied to a 3-pin fan on its Pin #2 varies from 12 VDC down to about 5 VDC, as the nerd 389 says. This causes the fan motor speed to change, according to the voltage supplied to it. A 4-pin fan works differently. For a 4-pin fan fed by a header using PWM Mode, the voltage supplied on Pin #2 is always 12 VDC, and the PWM control signal is fed to the fan separately on Pin #4. Inside the motor case the circuit board contains a small chip that applies the PWM signal to the power supplied as it flows through the motor windings, rapidly turning it on and off. The higher the % of the time that the PWM signal is on, the faster the motor can run.

If you plug a 3-pin fan into a 4-pin header that uses PWM Mode to accomplish control, the fan gets a fixed 12 VDC at all times on Pin #2, and does not receive (nor could it use) the PWM signal from Pin #4. So that fan always runs full speed. That is why a true 4-pin header cannot control a 3-pin fan. The opposite "mis-match" is a 4-pin fan plugged into a 3-pin header (or even a 4-pin header that is actually using Voltage Control Mode). In that case the fan receives a voltage supply on Pin #2 that varies, and it also receives NO PWM signal to use to modify the power it receives. So it just does what that voltage allows and behaves like a 3-pin fan, and its speed IS under control by the mobo. This is part of the backwards compatibility design of the newer 4-pin fans so they can run using older 3-pin fan headers.

Whether a 3-pin fan can be controlled by a mobo header with 4 pins depends on what the BIOS is designed to do. The 4-pin header may be designed to use only PWM Mode, in which case it cannot control the 3-pin fan, and that fan will always run full speed. Or, the BIOS may be designed to allow you to choose whether it uses PWM Mode or Voltage Control Mode (aka DC Mode), and setting it properly WILL allow that header to control that fan's speed. Or - third option, and VERY common on many mobo SYS_FAN headers - the 4-pin header may only operate in Voltage Control Mode despite having a 4th pin that it basically does not use. So it controls any 3-pin fan, but also it controls any 4-pin fan because of that backwards compatibility feature. That "universal control ability" is why so many mobos have been designed that way, and it works for most fan systems. It has two problems: (a) it fails to use the improved performance of true PWM fans under certain conditions; and, (b) it provides no PWM signal on header Pin #4, and that signal is REQUIRED if you try to use a 4-pin fan HUB device to connect several 4-in fans to that header.

So, yes, a mobo CAN power and control the speed of any 3-pin fan IF it is designed to do that. But a 4-pin fan header that uses only PWM Mode cannot control the speed of a 3-pin fan.

[strike]This is true. Your motherboard only supports 4-pin speed control, and only supports that on system fan headers 1 and 2 and the CPU fan header.[/strike]

I was corrected, see below.

Sorry, I neglected to note you had specified your mobo so I could look at its manual. I disagree with the nerd389 on your mobo's fan control capabilities.

On p. 1-20 of your manual its labels for the CPU_FAN header show it has a fixed 12 VDC signal on Pin #2 and "Speed Control" on Pin #4. This is a PWM Mode control system for your CPU chip cooler.

The labels for the SYS_FAN1 and 2 headers show "Speed Control" on Pin #2 and "NC" (no connection) on Pin #4. These two headers are using Voltage Control Mode, and that CAN control both 3-pin and 4-pin fans.

I agree that the SYS_FAN3 and 4 headers provide NO ability to control anything, and should not be used for your fans.

I stand corrected. You can plug the fans into SYS_FAN1 or 2, and speed control will work.

The Corsair Link Commander Mini will work, supports 6 fans, let's you place the temp sensors where you want them, and has mature software control. It also has an RGB header, if that's something you're interested in.

There are cheaper options, but most won't have software control.

That should work. You won't be able to monitor the fan speeds, but you can control the speed with it. The only down side is that you'll have to plug it into the CPU fan header. You should run a 4-pin splitter so the CPU fan can run off of the CPU header at the same time.

Yes. The splitter has one connection that's missing a pin. Plug that one into the controller hub, and the one with all 4 pins into the CPU fan. The missing pin is the speed sensor.

If you plug it in the other way around, you won't be able to read the CPU fan speed.

Wait! You don't meed a Splitter. That Phanteks PWM Hub will do it all for you.

When using that Hub, you unplug your CPU cooling fan from the CPU_FAN header and then you plug one of the Hub's cables (the one with a 4-pin fan connector on the end) into the CPU_FAN Header. Then you plug the other Hub cable into a SATA Power Output connector from your PSU, and that is where all the power for the Hub's fans is drawn.

The Hub's Port #1 is white, unlike the others, and is the only port that can report its fan's speed back to the mobo header. So it is important that you plug into that white Port #1 the actual CPU cooling fan. That way the mobo's CPU_FAN header will receive the proper fan speed signal. Then the Hub has five other ports on it, which happens to suit your situation nicely - you can plug your case ventilation fans into them. (Actually, it is possible to use splitters - two are included with the Hub - to connect two fans to each of those five ports if you need it.) The Phanteks Hub is unique among 4-pin Hubs because it does not merely share the PWM signal from the mobo header to its fans - that would require that you use 4-pin fans. Instead, this Hub uses the PWM signal to create its own group of six 3-pin fan headers that use Voltage Control Mode, which is exactly what you need to control your 3-pin fans. (That method also can control 4-pin fans.)

If you use the PHanteks hub in this way, ALL of your fans - CPU and case vent - will be powered and controlled by the mobo automatic system, based on the temperature inside the CPU chip. But only the speed of the CPU cooler will be mesured and displayed. The other fans' speeds will not be available.

3-pin and 4-pin speed control operate at different frequencies. 3-pin fan control does not work nearly as well as 4-pin fan control on a 4-pin fan.

When the option is available, 4-pin fan control is always the better option. If you use 3-pin control on a 4-pin fan, you will have to deal with the fan turning off entirely at lower speeds. With 4-pin fan control, the fan will instead turn at it's minimum speed when the speed control tries to run it slower than that.

It's up to you, but for a CPU fan, I prefer to play it safe.