Hi Mark, Thank you for responding so rapidly. I should note that identical processing (I use a script) on the trajectories produced by slightly different chemical systems had no problem and trajconv produced a complete processed trajectory.
However, when processing the problematic few with trajconv, the trajectory that is output is incomplete (the trjconv output has fewer frames than the input trajectory). This is definitely not problem with the change in output frequency of progress reports to the terminal. I am not sure if the -b flag is telling me anything. I move it around and it still seems to get stuck. I have ~30,000 atoms in my system. The first 120 ps are processed in ~ 5 seconds. The next 4 ps take ~ 30 sec. My trajectory is many nanoseconds long. Again, my other chemically similar systems do no hang like this and the simulation procedure is scripted so it is consistent across my different chemical systems. I am using gromacs/4.6.5. Best, Eric On Sun, Oct 26, 2014 at 5:21 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > The output does drop in frequency at some point, so that might be all you > are seeing. Experiment with -b and values around the putative problem area. > > Mark > On Oct 26, 2014 6:59 PM, "Eric Smoll" <ericsm...@gmail.com> wrote: > > > Hello Gromacs users, > > > > I have a trajectory file script18_o.trr that I am trying to process. > Using > > gmxcheck, this file appears to be complete. When I execute the command > > below > > > > trjconv -f ../script18/script18_o.trr -s ../script17/script17_o.tpr -o > > tmp1.trr -pbc whole << EOF > > 0 > > EOF > > > > the code moves quickly through the first few hundred frames only to > > consistently get stuck on frame 300... > > > > trn version: GMX_trn_file (single precision) > > -> frame 320 time 128.000 -> frame 300 time 120.000 > > > > How do I troubleshoot the problem? > > > > -Eric > > -- > > 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. > -- 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.