Re: AMBER: Scaling for octahedral versus rectilinear boxes

From: David Cerutti <>
Date: Fri, 31 Aug 2007 06:27:38 -0700 (PDT)

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


P.S. Any word on how much better AMBER10 PMEMD will scale than AMBER9?
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Sep 02 2007 - 06:07:30 PDT
Custom Search