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

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 17 08:50:01 CET 2003

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.
> John Stone:
> >The main thing we lack is a means of determining the _origin_ of the
> >unit cell.  Any suggestions on how to guess the origin of the unit cell on
> >file formats that don't provide it to us?  Several of them only give us
> >a/b/c/alpha/beta/gamma per-timestep, but nothing more.  If we can get the
> >origin of the unit cell, then it would be very simple to add the code to
> >draw the unit cell for ya.
> Thanks.
> Catch ya,
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
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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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