[gmx-users] Unexpected trjconv -nojump behaviour

[Tsjerk Wassenaar]

Hi Trayder,

The first frames did not have the same position/orientation and/or the same
box.

Cheers,

Tsjerk
On Mar 31, 2015 10:00 AM, "Trayder Thomas" <trayder.thomas at monash.edu>
wrote:

> 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
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