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.
