[gmx-users] drawing boxes

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 17 09:09:01 CET 2003

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 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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