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 <[email protected]> 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" <[email protected]> > 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 [email protected]. > > > -- > 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 [email protected]. > -- 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 [email protected].
