Hi PAULAMI, Use gmx trjcat to concatenate the two trajectory files and then calculate the rmsd. http://manual.gromacs.org/programs/gmx-trjcat.html
Best wishes, Tarak On Thu, Jul 9, 2015 at 1:34 PM, PAULAMI CHATTERJEE < chatterjee_paul...@yahoo.co.in> wrote: > Dear All, > I have a 30 ns trajectory which I would like to extend up to 100 ns. For > that I gave the following commands > gmx convert-tpr -s md_0_1.tpr -extend 70000 -o final_monomer.tpr > gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append > After completion of the extension two new trajectory files were generated- > 'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the > trajectory with > gmxcheck -f traj_comp.xtc > the output is > Checking file traj_comp.xtc > Reading frame 0 time 30000.000 > # Atoms 16867 > Precision 0.001 (nm) > Last frame 35000 time 100000.000 > > This trajectory file contains coordinate values from 30ns to 100ns. I > tried to calculate the rmsd with this file (both the trr and xtc file) but > the graph abruptly starts from 30ns (instead of 0) and continues upto > 100ns.For the calculation I need the total trajectory from time 0 to time > 100ns.I think I am missing something. > Can anyone please suggest anything here? Which one is the total trajectory > file then? > Thanks in advancePaulami > > > -- > 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.