[gmx-users] drawing boxes

[David van der Spoel]

By the way,

a problem in drawing boxes is how to deduce which shape a
non-rectangular box has. Given the box matrix one can deduce *for
gromacs* whether it is a truncated octahedron, or rhombic dodecahedron.
However, the coordinates are stored in the triclinic cell format, unless
they are converted back to the compact format (trjconv -ur compact).
So given the box there are still two possibilities. As a user I'd like
to make an animation of my protein in the dodecahedron, but to do that I
must back convert my trajectory. It seems therefore wise to let the user
choose the box rather than try to deduce it intelligently...

Hope I make myself clear, the PBC stuff is quite well described in the
GROMACS manual.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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