Re: [gmx-users] Unexpected trjconv -nojump behaviour
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.
Re: [gmx-users] Unexpected trjconv -nojump behaviour
Hi Trayder, 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? The idea of what jumped may change quite a bit if you have a 2nm shift. Also, nojump only keeps things whole if the molecules are whole up to PBC shifts. And they aren't as you find from your output. 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. The routine takes the first atom and then sees whether following atoms need to be moved over. 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. Probably. The routines are quite clear (and simple, and bugfree). This usually means there is a mismatch somewhere, between reference and trajectory or between successive frames. Try these two things: Visualize the .tpr and the first frames with the box and see what unjumping could do. Extract the original first frame from the trajectory and make that whole, then use that as reference with -pbc nojump. Cheers, Tsjerk -- 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.
Re: [gmx-users] Unexpected trjconv -nojump behaviour
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 tsje...@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.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. -- 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.
