Sorry guys but I do not get this...
I used: 1. First make your molecules whole if you want them whole trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc (I have chosen my whole system for input and output) 2. I do not need cluster anything 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o md2wholeDUMP.xtc ??? I did not obtain any coordinate file as output can be only trajectory (trr or xtc file) 4. How to use this frame in: trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o md2wholeDUMPnojump.xtc ????? Please, help! Steven On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi, > > You don't need a .tpr file for removing jumps; a pdb/gro file will do. > > Cheers, > > Tsjerk > > On Oct 24, 2011 2:51 PM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: > > Steven Neumann wrote: > > Dear Gmx Users, > I am trying to convert my > trajectory using trjconv. ... > trjconv -dump 0 > > > > 3. Remove jumps if you want to have them removed using the first frame > > > > trjconv -f traj... > Recreate the .tpr file using the coordinate file produced in (2). > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 >
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