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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