VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jul 21 2008 - 19:50:24 CDT

On Mon, 21 Jul 2008, Cesar Avila wrote:

CA> Dear VMD users,

cesar,

CA> I wonder how can I calculate the transformation matrix to obtain the +z
CA> periodic image of a triclinic box.

to do this from inside VMD is a pretty tricky issue unless
the original box is aligned in a specific way. VMD reads and stores
internally only the information about the length of the cell vectors
a, b, and c and the three corresponding angles alpha, beta, and gamma.

but the orientation vector of the box in space is missing, so it
is assumed that 'a' is collinear with the x-axis, 'b' in the
xy-plane and 'c' to span a right-handed coordinate system.

many solid-state codes re-orient structures for more efficient
calculations and thus the .cube and .xsf plugins undo this
rotation in order to get correct 3d periodic structures displayed
with VMD's periodic option.

so if your system is correctly oriented, you just need do translate
in x-, y-, and z-directon corresponding to the a, b, and c vectors.
of course the translations are additive...

cheers,
   axel.

CA> Thanks in advance
CA> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.