[gmx-users] trjconv -center -pbc whole ?!?

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 29 09:06:01 CET 2004

On Thu, 2004-01-29 at 04:01, Dallas Warren wrote:
> Has something changed with trjconv?  I can't for the life of me get it to 
> center a particular molecule within the box!  It sticks the molecules 
> selected to an edge of the box (~0 for z-axis, but box max for x and y), 
> not at the geometrical center/origin of the box.
Did you check the coordinates with gmxdump or so? There's a bug in ngmx
that shifts molecules when their coordinates are correct, so ngmx is not
a good test...
> Command line used:
> trajconv -f traj.xtc -o traj_centered.xtc -n index.ndx -s topol.tpr -center 
> -pbc whole
> And then, as it requests, select the molecule to center on from index file, 
> followed by the output file atoms.
> 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
> --------------------------------------------------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a nail.
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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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