[gmx-users] Unexpected trjconv -nojump behaviour

[Trayder Thomas]

The box is identical (copy+pasted), the orientation varies no more than one
would expect frame to frame (membrane protein). There is a 20 A jump
between the first and second frame but shouldn't -nojump still be keeping
the protein whole?

And shouldn't -pbc mol be keeping my "molecule" together? Even if its doing
it by fragments, I can't reason why it would take a fragment almost
completely inside the box (<1% atoms outside) and place it on the opposite
side of the system.

In the past I've managed to keep the protein together by running pbc mol
whilst centering on a residue at the interface between the two fragments,
but that's not working in this case.

I realise the system is trickier than most because its a rhombic
dodecahedron with the protein fitting quite tightly, but I've run dozens of
batches of simulations and only 2 are causing me any trouble. I can only
assume I'm making some invalid assumptions about how the commands work.

-Trayder

On Tue, Mar 31, 2015 at 7:15 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>