[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.
________________________________________________________________________
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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