AMBER Archive (2007)

Subject: Re: AMBER: Scaling for octahedral versus rectilinear boxes

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Fri Aug 31 2007 - 08:27:38 CDT

The reason I ask is that I've noticed that many systems aren't actually
that much better off in a truncated octahedron versus an orthogonal
box--for my Streptavidin system, for example, the difference in atom count
is 20%. In that system, the longest dimension of the molecule is about
1.2 and the system is fairly boxy-shaped to begin with. For a system like
Barnase:Barstar, where the ratio of the longest to the next longest
dimension is much larger, perhaps as much as 1.6. In the latter case, I
would expect the orthonormal box to actually solvate the system with fewer
atoms.

Dave

P.S. Any word on how much better AMBER10 PMEMD will scale than AMBER9?
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