Folding Forum

Hey I know I haven't been on here in a long long time. I just returned to ask a quick question that's been bugging me. That is, what does a WU actually look like? I know a WU consists of a bunch of calculations, but I wondering what one of them looks like and how many are in one WU? I return to the home site every once in a while checking progress on the results. Hoping that the project will be close soon to completion for one of the diseases it's working for.

First off, a WU is the actual data that the client is being asked to process. A WU consists of basically an iterative loop, which your computer then runs through, and returns the results of the calculation back when its done. How many iterations it takes to complete the WU varies. Work is being done on the new v7 client software, which will have the ability to display the WU in progress. It doesn't work right just yet, but when it does it will show you the protein you are folding in action, which will be neat. So basically a WU is just calculations being done on a protein, trying to simulate all of its movements.

Instead of the amount of calculations, donors often measure their contributions in terms of points. This matters because some WUs can consume a lot of other resources (such as RAM) while they are completed quickly, while some are pretty lightweight but take a long time. Some WUs have high scientific value/priority, so they have more points associated with them. The points make things a competition, which drives the project overall.

F@h is making outstanding progress, and I am very impressed with its accomplishments. Not only has it led to significant shifts in the understanding of protein folding, but it has produced a lot of results towards some of our scariest diseases. You're welcome to read about some of them on the main F@h page, but I've tried to outline SOME of them here: http://en.wikipedia.org/wiki/F@H#Biomed ... gnificance I'm confident that F@h will be making some big breakthroughs.

You want equations?

I'm not a scientist, but I do remember some high school chemistry and physics. To give credit where credit is due, this is my memory of something Bruce wrote a long time ago and I can't find it any more.

Suppose you know the mass, position and velocity of every atom in the simulation. Suppose you have some (very complex) equations that describe the forces on each atom. For every atom, apply the simple equation

F = mA+[rnd] except you have to solve for A, so it looks like A={F-[rnd]}/m

At any temperature greater than absolute zero, there is some random motion, and that's characterized by the term [rnd].

Numerically integrate that equation. That means that for a very short time period ΔT, the position will change by ΔT*velocity and the velocity will change by ΔT*A. Repeat for every atom. Repeat for each time period ΔT until it adds up to a total of whatever simulated time is needed.

Since the total time needed is too long for any one person to complete, break up the total trajectory into a series of segments and number them as sequential Gens.

For a more details or a more accurate scientific description of the equations, read the papers.

Or you could read this: http://folding.typepad.com/news/2007/09 ... rks-1.html which is somewhat simple. The papers can get really complex really fast.

Thanks guys. The combination of the last two replies pretty much answers my question. Just out of curiosity though, what are the papers that you guys speak of and where are they?

Results page link, from fah home page.

http://folding.stanford.edu/English/Papers