[gmx-users] Unexpected trjconv -nojump behaviour

[Trayder Thomas]

Hi,
I'm struggling with pbc nojump for a particular starting structure and
don't understand why.
The system starts with a broken conformation so I've concatenated it onto a
whole structure such that the whole structure is the first frame:
trjcat -f whole.xtc md1-1.xtc -cat -o test.xtc

I then look at the resulting file and it's exactly how I'd expect.

I then run trjconv with nojump
trjconv -f test.xtc -pbc nojump -o test2.xtc

Looking at the output from this, the first frame is fine but on the second
frame some residues of my protein that were near the boundary immediately
jump to the opposite side of the periodic cell and stay there.

When I try to fix that with pbc mol:
trjconv -f test2.xtc -pbc mol -s system.tpr -o test3.xtc

I find that half of my protein (2 fragments under one molecule type)
instead jumps across the system to follow the few stray residues.

Any ideas?
Thanks,
-Trayder