On Sun, Oct 26, 2014 at 11:44 PM, Eric Smoll <ericsm...@gmail.com> wrote:
> 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. > The point is to try to see whether the issue happens x steps into the trajectory, or only at around t=120ps. Does it happen if you are using -pbc somethingelse? Does it happen if you copy the file to some other filesystem before using -pbc whole? One needs to find a pattern before one can guess where the problem might lie. > 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. > OK. It's possible your simulation system is doing something pathological in that trajectory, which somehow does not agree with the implementation of -pbc whole (I'm guessing wildly here), but one would need to try the above kinds of experiments to probe that, and or visualize the trajectory in some viewing program. Mark 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. > -- 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.