[gmx-users] Where is the origin of the coordinate system?

David van der Spoel spoel at xray.bmc.uu.se
Mon Jul 9 13:34:25 CEST 2007

Lam Nguyen Sy wrote:
> Dear Gromacs users,
> I have a problem on understanding where the origin of
> the coordinate system is. Is it at one corner of the
> box, at the center of the box, or somewhere else? The
> box type I'm using is truncated octahedral.
> I tried to find the minimum and maximum coordinates of
> a system (including proteins+water), and it turned out
> that the minimum was close to 0 and the maximum was
> close to the length of the box vector. This meant the
> origin was at a corner of the box. 
> But in my analyses, when I pretended that the origin
> was at the center of the box, the result appeared to
> be very good. And the much worse resulted when I used
> the origin at a corner of the box.
> If there is any idea, it would be very useful for me.
> Have a nice week,
> nslam

it is at the origin of a cubic box in which your trunc oct fits.
you can translate everything if you wish by trjconv. try out g_traj for 
analysis as well.

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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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