Dear Gromacs Users, To avoid pbc in my trajectory file I used command:
trjconv -f md.trr -s md.tpr -pbc mol -ur compact -center -o md.xtc I have choosen protein to be centered. Everything is ok with my protein which does not jump and remains centered in the box. However, some of my ligands change their place in given frame VERY rapidly... I had the situation like this before the command above with my protein as well which now is stable... Any suggestions please? Steven
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