F@H Basics
Folding@home is the name of a project under the direction of Professor Vijay Pande at the University of Stanford in Palo Alto, California. The goal of the project is to better understand the molecular dynamics of proteins and other molecules’ folding processes through both theory and simulation. You can see Pande Labs’ own description of their work, as well as their affiliated laboratories and commercial supporters here.
Protein folding is a very complex and critical process in biology and has only in recent years been able to be modeled at all due to the large number of variables involved. At each step in the modeling process the properties (which I disuss here) of every piece of the molecule and its surrounding media must be evaluated against every other property. Greater numbers of molecules in the simulation increase its accuracy but exponentially increase the amount of computer work that needs to be performed in the simulation. Time is another major factor, as the longer the simulation needs to be the more computing horsepower is necessary to make it happen.
In recent years the concept of Distributed Computing has evolved. Distributed computing is the concept of breaking a very large computer problem up into very small pieces and sending those small pieces to computers elsewhere to be calculated and then having the results of the work sent back. Folding@home is a distributed computing project where a number of large simulation projects are broken into small pieces and the work is sent to the standard desktop computers of volunteer individuals and companies around the world. These volunteers’ computers model their tiny pieces of the simulation and then return the work to Stanford University where it is reassembled into a whole. The simulations are then used in scientific research and theorization, some of which can be seen here.
Anyone with a Windows or Linux computer and access to the Internet can download the Folding@home software, called a “client” and install it on their computer. The client will run in the background or as a screen saver and run the simulation math only when the computer would otherwise be idle. The client software is designed to be unobtrusive and not interfere with a user’s normal work with his computer in any way.
As computing, and in particular computer gaming, has advanced, the graphic cards used in personal computers to create 3D graphics have become tremendously powerful computers in their own right. In fact, the newer generations of graphics cards from nVidia and ATI are substantially more powerful than a computers’ main processor because they have many fast computers in them that work in parallel. The gaming card pictured here is the nVidia GTX295 which by itself has an astounding 480 computers onboard operating simultaneously. Just as amazingly, it can be bought for less than $500.00.
To harness the speed of volunteers’ Graphics Processing Units (GPUs) for their simulations, Pande Labs has created a version of Folding@home that runs on the video cards instead of the main CPU. This GPU version of the software is also easy to install and run behind the scenes. It is this version of the software that Atlas Folder runs and why it requires many graphics cards to be as powerful as it is.
Running Folding@home has become something of a competitive sport, as the software allows for the formation of teams whos total contributions to the project can be monitored here. Users can see their team’s output in relationship to other teams, as well as compare their individual output to their teammates’. Atlas Folder folds for the HUNT-DIS (Huntington’s Disease) team which is #36167 under the name AtlasFolder.
If you have an interest in volunteering your unused computer cycles to the Folding@home project (I hope!) there are a number of good tutorials on how to install the software. If you’re an experienced computer user you will find it relatively easy, but if you’re not a computer expert and would like some pointers, the following link will take you to the official Folding@home guide.
