[gmx-users] trjconv - Protein and jumping ligands

Steven Neumann s.neumann08 at gmail.com
Tue Aug 30 15:00:25 CEST 2011

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?

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