On 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 ?