[gmx-users] Origin in trajectory files (xtc/trr)

[David van der Spoel]

On Mon, 2003-11-17 at 17:50, Anton Feenstra wrote:
> David van der Spoel wrote:
> 
> > On Mon, 2003-11-17 at 01:33, Dallas Warren wrote:
> > 
> >>Have asked for the addition to VMD of the unit cell drawn on coordinate and 
> >>trajectory files.  Since I don't know the file formats that well can anyone 
> >>here provide an answer to John's question?
> > 
> > In gromacs it's at 0,0,0
> > I think in most codes it is at either 0,0,0 or
> > the center of the box.
> 
> Since a unitcell implies either a periodic box (PBC) or a (periodic)
> crystal, does it matter at all where the origin lies? In other words,
> what is your definition of origin?
You want the atoms drawn inside the box. So it does matter whether the
origin is at 0,0,0 or elsewhere.
-- 
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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