On Nov 2, 2009, at 6:28 AM, Keren Lasker wrote:
That isn't the question I have. Clearly fewer particles makes things faster :-) My question is: - We have a function which guarantees that consecutive residues are kept together along the backbone. By providing such a guarantee, it limits the set of simplified structures that it can produceOn Nov 2, 2009, at 6:10 AM, Daniel Russel wrote:I still have the question of why bother keeping consecutive residues together? As far as I can tell, it produces uniformly worse results than allowing them to be separate. Unless there is some advantage, it isn't something that should be there.I think we should separate the discussion for fine coarsening ( up to 5 residues) coarse coarsening ( more than 5 residues).For fine coarsening I think the helper function is fine and most restraints would work well with it.This is a way of accelerating the optimization. We can benchmark your updated excluded volume restraint for example to see how well it preforms with large assemblies - lets look at it today together - sounds good ?
- The more limited set is worse than a set not constrained by that guarantee under various various conditions and metrics discussed before
- If one has a group of residues that really need to be kept together, it is easy enough to simplify them separately from the other residues.
- As far as I can tell, the limited set is not better under any metrics/conditions that we care about. If this is the case, then we shouldn't have a function which simplifies along the backbone. And if this is not the case, I'm wondering when it is not :-)
So the question is when is it useful to someone to guarantee that consecutive residues are kept together?