Re: correction about solvateOct

From: Michael Crowley <>
Date: Fri 19 Jul 2002 09:37:10 -0700

SolvateOct iso does two things differently from without the iso.
First, as mentioned already, the truncated octahedron is isotropic,
same dimensions in all three principal directions.
Second, the truncated octahedron is rotated so that it is
ready for crystal-type periodic imaging. To be specific, the
three crystal directions (which are normal to three of the hexagonal
faces) are oriented so that one is on the x-axis, and another is
in the x-y plane.

The imaging in sander (bothe amber6 and amber7) requires this orientation
regardless of whether PME is used or not, but whenever periodic boundaries
are used (ntb=1). Perhaps future versions will go to a more general
unit cell description, but for now it is assumed that the
a and b unit cell vectors are oriented as described above, and
that one has the lengths of the a, b, and c vectors and the
angles between them in the coord or restart file to tell sander
what the unit cell is.

I hope that explains the use of iso and why it is necessary,
please ask for further explanation if it is needed.

Physical mail: Dr. Michael F. Crowley
                 Department of Molecular Biology, TPC6
                 The Scripps Research Institute
                 10550 North Torrey Pines Road
                 La Jolla, California 92037

Electronic mail:
Telephone: 858/784-9290
Fax: 858/784-8688
Received on Fri Jul 19 2002 - 09:37:10 PDT
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