Hi Xavier, By when do you need it? You can send me one frame ( .gro) and I can see what I can do. But no guarantees, and no time indication :(
Cheers, Tsjerk On Mon, Jan 26, 2009 at 7:11 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote: > >> Hi XAvier, >> >> Unfortunately, you're out of luck. The coordinates do not contain >> information regarding the proper orientation with respect to the >> coordinate system. > > No they don't. > > May be I should have mentioned that I know for each > conformation of the system (protein embedded in a membrane > bilayer) the exact transformation that has been that has > been operated: a rotation around the z axis. >> >> That's the short answer. I guess you did save all atoms, at least of >> proteins and lipids, in which case you could do a search for a >> rotation matrix that restores your PBC. If you have a brick or >> triclinic representation of your atoms the easiest solution is to fit >> planes through the sides, from which you can infer the original >> coordinate system. Then you can rotate that back to match the one >> stored. > > The other option I found is to duplicate the system on x and y > directions, then center a copy of the protein and finally put everything > inside the new cell (made up from 4 copies of the original cell). > Then when rotating the pbc and included on the x and y directions. > > Thanks for you thoughts I knew you'd had but I hope for a magic > solution. > > Best, > XAvier >> >> Hope it helps, >> >> Tsjerk >> >> On Sun, Jan 25, 2009 at 7:43 PM, XAvier Periole <x.peri...@rug.nl> wrote: >>> >>> Dears, >>> >>> I need to rerun a trajectory that has been rotated to orient a molecule >>> according to a reference. The pbc are therefore broken. >>> >>> Would anyone know how to restore the correct position of the atoms inside >>> the unit cell after the rotation is applied. The rotation is actually >>> applied around >>> only one axis (z, membrane normal). >>> >>> Thanks for any suggestion. >>> XAvier. >>> >>> _______________________________________________ >>> gmx-users mailing list gmx-users@gromacs.org >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before >>> posting! >>> Please don't post (un)subscribe requests to the list. Use thewww >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> Junior UD (post-doc) >> Biomolecular NMR, Bijvoet Center >> Utrecht University >> Padualaan 8 >> 3584 CH Utrecht >> The Netherlands >> P: +31-30-2539931 >> F: +31-30-2537623 >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
