Run/Clone/Gen
Posted: Tue Dec 11, 2007 1:40 am
Hi.
I've been trying to figure out the concept of FAH. I read some of the older papers on the subject in the results section like No 4 for instance. This article said that different simulations make different progress, some may remain in a pseudo-stable state for long time, while others are more "productive". When simulation results are sent to the server, then a simulation which advanced the most gets picked and a new generation of simulations is based on it. A generation contains hundreds of clones, with the protein in the exact same folding state but the initialization parameters slightly different.
This article was published 4 years ago, so it was probably written 5 years ago. I beleive TINKER was still used back then. Now that most of FAH has migrated to variations of GROMACS, is the same approach still used? Every project has a Run/Clone/Gen id and the Clone and Gen part kind of hints that the methodology is not entirely dissimilar
but what exactly is a Run?
In the case I'm completely wrong here, are there any articles or forum posts available that discuss how FAH is parallelized with the GROMACS technology?
Thanks in advance.
I've been trying to figure out the concept of FAH. I read some of the older papers on the subject in the results section like No 4 for instance. This article said that different simulations make different progress, some may remain in a pseudo-stable state for long time, while others are more "productive". When simulation results are sent to the server, then a simulation which advanced the most gets picked and a new generation of simulations is based on it. A generation contains hundreds of clones, with the protein in the exact same folding state but the initialization parameters slightly different.
This article was published 4 years ago, so it was probably written 5 years ago. I beleive TINKER was still used back then. Now that most of FAH has migrated to variations of GROMACS, is the same approach still used? Every project has a Run/Clone/Gen id and the Clone and Gen part kind of hints that the methodology is not entirely dissimilar
but what exactly is a Run?In the case I'm completely wrong here, are there any articles or forum posts available that discuss how FAH is parallelized with the GROMACS technology?
Thanks in advance.