Useful Resources


  • Check the CPU Performance/Price list.

  • Look for something well represented on this list

  • Or look for an equivalent model, especially one that’s just being discontinued for the next new fancy thing

  • Try to find a CPU/motherboard combo.

Here’s one: http://www.newegg.com/Product/ComboDealDetails.aspx?ItemList=Combo.1515357 Note that this is not necessarily a good CPU from my first tip, but I’ll let you find the convergence. But you can see that such things are out there. In one swoop, you get a better deal and solve any incompatibility problems between CPU and mobo. I picked this one because I wanted to make the point that I’m kind of a fan of ASUS. But use product ratings by customers wisely. They are worth paying attention to.

My very rough thinking these days (2015) is that AMD gives better performance per purchase dollar while Intel gives you better performance per watt. This may be backwards, but it highlights the thinking you should be doing. Note that a better performance per watt means a quieter machine, other things being equal.


  • Form factor needs to be right.

  • Enough USB ports?

  • SATA3 or whatever you need?

  • Note the power supply connector (pretty standardized now).


Next you need memory for the motherboard in question. One trick here is to look at the "others who bought X also bought" and look for memory. Note this is not fool proof. You have to double check. But it gets you started. You can also go to http://crucial.com and generate a compatibility report. Memory has about a dozen parameters that all must be compatible. But annoying as this can be, it’s actually not too hard in practice to home in on the right modules.

Keep in mind physical setting too. Many times memory modules with fancy cooling fins have a hard time coexisting with a large CPU cooler/fan.

Power Supply

Then you need a power supply. I don’t have a brand name here, but I look for user reviews that gush about the quietness. You’ll thank me.

Here’s a new thing to think about - just had a protracted power outage where 1/2 of my computers died and half didn’t. The odd thing is that not all power was lost; the voltage was cut in half down to 50-60VAC. I don’t know exactly how to test for this but handling a robust diversity of input conditions should be considered worthwhile.

Checking A Power Supply

Use a paper clip to short out the green wire with an adjacent black one. If the fan comes on, the power supply isn’t completely dead.

Specialized testers are also quite cheap and can properly test all aspects of the unit.


Fans suck. Fans fail about twice as often as mechanical hard drives and for often the same reason, mechanical wear. Fans are noisy and bulky. If at all possible it is best to prioritize fanless designs. If that is not possible, buying high quality fans or parts using them is not wasted effort. The larger the fan is, the slower it can turn to move the same air. The slower it turns the quieter it is. The small high speed fans are not just noisy, but obnoxiously high-pitched and especially prone to failure. This can be especially awful on GPUs with small fans.

Case Fans

Case fans are strangely challenging to measure properly. Look at the signal and noise here.

I think the nominal sizes for fans should be measured along one square edge in mm. Here are sizes I know about.

  • 80mm - a relatively small fan that I can’t find much use for. Maybe good for some GPUs. Found one on a special internal case fan. Approx. 101mm bolt circle diameter.

  • 92mm - the most common case fan despite the non round number. Approx. 117mm bolt circle diameter.

  • 120mm - a relatively big fan, often the kind filling the entire width of a power supply. Approx. 148mm bolt circle diameter.

The next worry is the connector. Those come in two flavors.

  • molex hard drive - 2 wire (fun fact, they’re AMP, not really Molex).

  • motherboard header - 3 wire

GPU Fans

While these are always the first things to fail on a GPU, on a cheap card it is unlikely that you will be able to replace the fan for less than you can just buy a new card. On expensive cards, the bigger the fans, the quieter and slower they will be and the less likely to fail prematurely.

CPU Fans

If the CPU didn’t come with a fan, you’ll have to buy that, but I’d say it’s pretty rare these days for the fan not to be included with the CPU. You pay $150-500 for 50g of plastic - they (Intel/AMD) can throw in a $5 fan. That said, fancy oversized heat sinks can really help keep an otherwise noisy whiny CPU fan under control.

These CPU fans can be a pain to match. This is extra annoying since they are the #2 thing to fail (after GPU fans and tied with PS fans).

The following good description of the situation is taken from this article.

  • Intel LGA775: Unfortunately, Intel heat-sink/fan combos differ across generations. If you have a LGA775 socket CPU, it will require either an LGA775 compatible Intel heat-sink/fan combo, or a complicated “universal” after-market HSF. An exception to this rule is the transition between LGA775 and LGA1155. You can also use LGA1155 heat sinks on LGA775, although there may be some compatibility issues, particularly with bracketed coolers.

  • Intel LGA1155: In general, Intel did not rationalize its fan design. Intel tends to use a different heat sink for each of its CPUs. However LGA775 and LGA1155 HSFs are mostly cross-compatible. The new Haswell LGA1150 socket appears to also work with LGA1155 and LGA11775 sockets.

  • AMD AM2, AM2+, AM3, AM3+, FM1 and FM2: Conveniently, almost all modern AMD socket types use interchangeable CPU heat-sink/fans. If you have one of these AMD models, almost all heat sink/fans work interchangeably, provided they can handle the heat produced by the CPU.

An even more simplistic breakdown is this.

  • AMD - square holes that latch onto the plastic base, often with a cam.

  • Intel - four wonky plastic push pins sort of snap into the motherboard.

Trying this one for low profile.

Used this one to successfully eliminate high load noise on two machines (AMD and Intel): Enermax ETS-N30R-HE Note that to install one of these you usually need to remove the motherboard to replace the CPU mount backplate which is included with the fan.

Hard Drive

You need a hard drive, but this is not really a critical component. You can freely change this around any time. Consider buying two 1.5TB drives instead of a 3TB drive. Or buying a small solid state drive and a large mechanical drive (speed and capacity respectively). For hard drives, a long warranty is good (3 years or ideally 5). Even a very small $50 hard drive will get you going just fine and you can add drives as you need them for actual capacity. Or start by running only Linux from USB sticks and buy hard drives when the need arises and is better specified.


Also a secondary note about a couple of second-tier drive vendors changing the components in some of their drives after the reviews have been published.

Video Card

Most motherboards have a built in video chip (the GPU I spoke of). But this will often be an Intel graphics chip which are much lamer than Nvidia or ATI. I would strongly favor Nvidia which is really the gaming standard (and important for molecular visualization in my case). Be careful with video cards since they often have little fans which means faster rotation to do the job. And that means higher pitch (whiney). These fans are premounted on the card. Try to find reviews that are happy with the low noise of the GPU fan. Also, lots of video RAM is good (1GB should be a minimum these days probably). I actually like the GeForce 8400 http://www.amazon.com/EVGA-GeForce-Passive-Graphics-01G-P3-1303-KR/dp/B004KABG18 Because it is fanless and dirt cheap. These cards never fail and have surprisingly great performance (as good as a PS3, for example). But check specks and see what the latest hype is. I see that this has DirectX 10 and you might want DirectX 11 these days for the new breed of games that will be coming. If you’re a molecule worker, these passive cards work great.

Wondering how awesome your awesome GPU is? Check out GPUBench.


Then you need a case. It can be decent to buy all the other stuff first and assemble it on a table top and just make sure it all works. Then its simply a matter of buying a case with the right "form factor", probably ATX https://en.wikipedia.org/wiki/Computer_form_factor Oh, and make sure your power supply and motherboard agree about form factor.

I recently was impressed with a be quiet Silent Base 800 case that went out of its way to dampen vibrations. A lot of time noisy computers are a result of resonant frequencies from fans and hard drives vibrating the panels of the case like a speaker element. Cheap low tolerance, light weight cases will suffer more from this problem. Expensive cases will suffer from being expensive.