AMBER Archive (2007)

Subject: AMBER: Scaling for octahedral versus rectilinear boxes

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Fri Aug 31 2007 - 00:32:49 CDT

Hi,

I think I know who can answer this, but I'm going to the listserv so the
knowledge can be spread around.

Do simulations with truncated octahedral boxes scale as well to many
processors as those with rectilinear boxes?

On the one hand, the neighbor list may level the playing field, but on the
other, there may still be some need for a domain-decomposition style
computation to generate that list, and the best thing to have then would
be an orthonormal box.

Thanks!

Dave
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