Daniel Russel wrote: > Frido was complaining that the nbl was too slow, so I thought I would > check in my local changes. The big thing is that the fastest > implementation I have uses the CGAL library.
All patches to IMP need to be reviewed before they are checked in. Obviously, I am not going to do this while I'm on vacation, so unless somebody else with some understanding of the code volunteers to check through these patches, they'll have to wait until I'm back in the lab.
I don't think we can use CGAL. It is certainly available for Fedora, but we build on a lot of other platforms too. And my understanding is that large chunks of it are QPL licensed, which is certainly incompatible with the IMP license. If we did use it, we'd have to be very careful to use only the LGPL parts. So I'd rather we didn't use it at all.
Your timings suggest that the current grid nonbonded list implementation is not O(N). Why not? It seems like it should be from my understanding of the code.
Ben