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

nahren manuel meetnahren at yahoo.com
Wed Apr 22 11:06:22 CEST 2009

Dear Gromacs Users,
I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns. 
I then concatenated the two trajectories using trjcat
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. 
2. The box seems to shift from one corner to the center. Especially for the duration 8-12 ns (my restart run)
I feel I am missing something here. Kindly advice.

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