Algorithms used in folding?

[aceface57]

Does anyone know what algorithms stanford use in their code, the reason i am asking, is i am doing an honours in genetic algorithms for mobile platforms, with a view in chemo optimzation. If it is genetic algorithms i would love to find out more about their souce code and i could possibly get my uni intersted in the project (they know very little about folding). Any info is much appreciated

 

[SiriusB]

The source code is a secret as they don't want any herbert to be able to tinker and possibly cause problems.

As for specific algorithms I suggest you have a look at the FAQ on stanfords website, or try the forums, there may be some info there.

SiriusB

 

[rich99million]

The main tool they use is Gromacs which is licensed under the GNU General Public License so that may be of use to you.

http://www.gromacs.org/


As SiriusB said though, Stanford's own implementation is closed source so you're unlikely to get any specifics out of them.
You may find someone willing to discuss the subject on the main forums http://forum.folding-community.org/forums.html

 

[BillytheImpaler]

Stanford's implementation contains very few changes in therms of the actual MD loops. Their changes most likely involve MD5'ing the WUs so as to determine if they're corrupt and things like that.

Some other cores that are (or were) used:
QMD (CPMD): http://www.cpmd.org/
Tinker: http://dasher.wustl.edu/tinker/
Amber ($400 for educational use): http://amber.scripps.edu/#code