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.tho...@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-requ...@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-requ...@gromacs.org.