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.
regards,
nahren
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