[gmx-users] Origin in trajectory files (xtc/trr)
David van der Spoel
spoel at xray.bmc.uu.se
Tue Nov 18 09:26:01 CET 2003
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 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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