AMBER: Octahedral box orientation

From: David Cerutti <>
Date: Tue, 21 Aug 2007 06:08:38 -0700 (PDT)


    I'm trying to determine the way the truncated ocathedron is oriented in
the AMBER code. From visualization, it appears that the octahedron is
oriented with one of its hexagonal faces in the XY plane, but I can't even
be sure of that. Just having coordinates does not really tell me where
the boundaries of the simulation box really lie. The one thing I've got
going for me is that I am using a regular trucated octahedron for these
simulations, so the square faces are really squares and the hexagons are
regular hexagons. Can anyone show me how to reconstruct the locations of
the truncated octahedron vertices based on the three dimensions given in
each snapshot of the simulation coordinates?


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Received on Wed Aug 22 2007 - 06:07:46 PDT
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