Dear Sir, First trajectory - traj1.xtc (0 to 5... ns) Second trajectory - traj2.xtc (5... to 25ns)
But there is no gap in between. for concatenating - $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc For nujump - $ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc I also have a case where I ran 10ns in 64 cores and later continued in 8core machine. This also has the same problem. While running in 64 cores by default it did not generate the checkpoint file. So I has to use tpbconv to generate a new tpr file for continuing from the same point - $ tpbconv -s old.tpr -f traj.trr -e ener.edr -o new.tpr Thanks in advance. Regards Kavya On Thu, Aug 1, 2013 at 12:20 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Kavya, > > That shouldn be a problem. Please post your sequence of commands for > concatenating and further processing of the trajectory. > > Cheers, > > Tsjerk > > > On Thu, Aug 1, 2013 at 8:12 AM, Kavyashree M <hmkv...@gmail.com> wrote: > > > Dear users, > > > > I ran a simulation for 25ns. First 5ns in 8 core machine > > and late part in 64 cores. It ran without any problem. The > > trajectories were concatenated, jumps are removed and > > rmsd was calculated. But there was sudden jump in the > > rmsd curve. Is it wrong to run simulations in different > > cores like this? > > > > Thank you > > Regards > > Kavya > > -- > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 > -- 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