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Re: [IMP-dev] NBL cleanup and other small patches



one possibly ignorant question: andrej got along without fancy libs.
knowing him, i presume he stole the code from somebody else. can't we
simply do the same? the code was pretty fast...
:-) The modeller code doesn't work because it assumes equal sized particles.
Exactly, although where we do have atomistic systems, this would still 
be a reasonable assumption.
He also claims he put a fair bit of effort into optimizing it.
I think that's a little generous! It's just a standard cell-based 
algorithm. The only optimization I see in the code is on the hash 
function, and that's still a very simple function.
The Modeller code probably gets most of its performance from having 
optimizers that are cooperative. In order to tell whether a nonbond 
update is required, a simple heuristic is used: has any atom moved more 
than some cutoff distance since the last update? This is easy to test 
for because all of the optimizers update this atom shift value whenever 
they move an atom. In IMP there is no such guarantee - the optimizers 
write back new values for the optimizable attributes whenever they feel 
like it (plus, of course, we have attributes other than xyz).
	Ben
--
ben@salilab.org                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle