Folding Forum

You're so over the top exuberant about supporting fah, and then you post these comments coming down on fah? Strange.

How hard is it to grasp that PRCG are not techical terms? They are not scientifically derived. They are simply common lables to represent complex concepts, not unlike x, y, and z for a 3 dimensional axis. Did you need to know anything more about x, other than it's the first horizontal axis? y is the 2nd, and z is the vertical. Technical, but simple.

PRCG is the same way. Simple divisions to represent samples of data used later in a more complex way.

I'll use some big words so that Dan's simple explanation seems more technical.

Project # is the numerical designation for the initial set of work unit parameters. Project numbers are not repeated (although they have been in the past, by mistake.) They are also numerically grouped by researcher / field of study.

Run is a numeric designation for groupings of Clones with identical work unit attributes, the exact same atoms, the exact atom positions, the same temperature, except for different (randomized) starting velocities.

Clone is a numeric designation for each trajectory, and "trajectory" is the very technical thing here. See the first paragraph of Dan's FAH Wiki article*.

Generation is a numeric designation for a pre-determined length of time along a trajectory (Clone) for a specific project.


*For reference, Dan wrote, "the key idea is that of a "trajectory." You might recall Newton's Second Law, F = ma, which means that the acceleration a (change in velocity) that a particle experiences is proportional (by its mass m) to the force F it experiences. This means that if we can catalog all the forces on a particle, we can determine its acceleration. If we know the acceleration, then we can use calculus to determine the particle's position as a function of time, for all time. The result is what's called a 'trajectory' -- a kind of map of where the particle has been and where it will be going."

Well if that's the way it is all the time then that's pretty handy. I just thought it was more scientifically grounded like that, and that there were more details. For example, Project 5749-5756 are all at different temperatures, so I guess that's their initial WU parameter and the Runs are unique with respect to atomic positions or something. So there it's starting to agree with Dr. Pande's response. I'd imagine that for things like Simulated Tempering and Free-energy Perturbation the numbers would probably mean something different. I was just trying to figure it out. Though I would have liked a detailed explanation (like "and when we do THIS, they mean THAT") but I guess the PG has to deal with all of these different parameters and the PRCG numbers just distinguish them all however the responsible scientist likes.

If they chose to make projects with different temps, then they may have locked down one of the other variables, as you suggested. But an small deviation from form does not invalidate their descriptions.

I also see where Dan said that Runs has an alternative meaning as well, but still fits in to the model of PRCG. As I see it, it's just one more way to adjust x, y, or z to experient with the shape of the resulting graphed solutions.

re-exploring is hyphenated.

A protein spends most of its folding time "stuck" in an energetically-favorable positions,

position should be singular

5... Quantitative com arison of villin headpiece subdomain simulations

missing a p

They have to be simulated from start to finish, but it would be impractical for one computer to complete one by themselves.

by itself.

What is adaptive sampling, and how do they related to MSMs?

Extra d