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18:27:26
drmeister
I'm trying to do a simple common chemical operation - compare the position of every atom to every other atom for a moderately large system of atoms - N^2 comparisons - that's 1Billion pairwise comparisons will take 20 minutes with Cando as it is currently setup.
18:29:17
drmeister
That's doing it the naive way, putting all of the atoms into a vector, looping over the atoms with an inner loop over the rest, pulling up the position of each atom and calculating the distance.
18:51:14
drmeister
The reason I bring this up is there are times when the naive approach would be very quick to implement but it's slow now because doing anything with double precision values or getting a vector conses memory. That slows things way, way down.
20:27:05
Lord_Nightmare
drmeister: sounds similar to what elmar krieger's YASARA thing does, except i don't know if that is lisp/clasp based
20:42:32
drmeister
Except they don't appear to be based an accepted molecular dynamics engine (AMBER in our case).
20:45:00
drmeister
Written in something called "Portable Vector Language" - do you know what that is?
20:55:28
Bike
i see a Scientific Vector Language used for computational chemistry, but it's proprietary
21:02:03
drmeister
They say they wrote YASARA in PVL - and there is little indication what PVL is. Weird.
21:10:01
drmeister
The thing about this molecular modeling stuff is you have to stick very closely with accepted tools and methodologies. Otherwise people won't trust it.
21:11:11
pnpuff
drmeister: High Performance Embedded Computing Handbook: A Systems Perspective (17.2.4)
21:12:05
pnpuff
is long ... https://books.google.it/books?id=6H50DwAAQBAJ&pg=SA14-PA71&lpg=SA14-PA71&dq=portable+vector+framework++pvl&source=bl&ots=CsRoBxZ5xI&sig=ACfU3U1qpn7YUuYHXE-XMtQeZfPYEUKMFA&hl=it&sa=X&ved=2ahUKEwin05Xu3dPkAhXQUlAKHWO0AIAQ6AEwDHoECAkQAQ#v=onepage&q=portable%20vector%20framework%20%20pvl&f=false
21:44:34
drmeister
Building a membrane that avoids a protein is much faster using our oct-tree code.