I use bellow commands but still in some of snapshot trajectories, two strand of DNA separated from each other in VMD.
trjconv -s md.tpr -f md.xtc -o md.pdb -center trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -ur compact trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center -ur compact trjconv -s md.tpr -f md.xtc -o md.pdb -center -ur compact On Sun, Jan 20, 2013 at 3:38 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/19/13 5:21 PM, Mehdi Bagherpour wrote: > >> hello everybody >> >> I have simulated DNA using CHARMM force field for 50 ns with 2 ps >> snapshots >> for each step. >> when I wanted to convert .xtc trajectory files to .pdb using trjconv, >> some >> of the snapshots were collaborated. >> I have used periodic boundary conditions in this simulations. >> To convert, I used bellow command: >> >> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol -center >> >> In collaborated .pdb files two strands of DNA separated from each other. >> when I used bellow command instead of above command, this collaborated >> .pdb >> file will be corrected, >> but some of the other .pdb files will be ruined as same as >> >> trjconv -s md.tpr -f md.xtc -o md.pdb -pbc mol >> >> would you please help me to solve this technical problem? >> >> > Use -center, perhaps in conjunction with some custom index group that will > serve as an adequate central group for processing. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
