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

Dallas Warren dallas.warren at vcp.monash.edu.au
Thu Jan 29 04:06:01 CET 2004

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.

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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