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Re: [IMP-dev] Nonbonded lists



Daniel Russel wrote:
Sorry, better answer:
You don't care about the radii for electrostatics, so you just ignore it when you pick your maximum search distance. The radius has nothing to do with energy evaluations, just with searches for nearby pairs.
Of course - but the radius attribute is used for both purposes. It seems 
weird to require the user to specify a dummy radius attribute for 
electrostatics (which, as you say, isn't needed for the actual energy 
evaluation) just to make the nonbonded list work. Plus, I imagine the 
nonbonded list can be made more efficient if it knows that all "spheres" 
are the same (e.g. have zero radius). So either we keep both sphere and 
non-sphere nonbonded lists, or the implementation can be asked to ignore 
the radii (not sure what your earlier email meant, but perhaps taking a 
FloatKey* and having NULL mean "ignore radius").
	Ben
--
ben@salilab.org                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle