[gmx-users] -center -fit dodecahedron : dimer

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 22 11:20:27 CEST 2009

Hi Nahren,

> trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc
> trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter tric -o center.xtc
> trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc

> 1. The above procedures does not center the molecule in the box.

You first center and then do a fit. The fitted trajectory will only be
centered if the reference (proem.tpr) is (and then you can skip the
second step anyway).

> 2. The box seems to shift from one corner to the center. Especially for the
> duration 8-12 ns (my restart run)

What do you mean with this?



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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