I have experienced something similar with large trajectories. This command got killed by 42 ns, with the same error. It is a 60 ns trajectory of a large membrane-protein system (approx 450000 particles, Gromos 54A7 ff) with data stored every ps.
g_msd -f analysis_60ns_pbcnojump.xtc -s analysis.tpr -o msd_popc_overall.xvg -lateral z -n index.ndx On Sun, May 19, 2013 at 1:57 AM, Yutian Yang <yyan...@syr.edu> wrote: > Dear all, > > I am using g_msd to calculate diffusion coefficient of the centre of mass > of single polymer chain with the following command: > g_msd_mpi -f 1.trr -s eqm.tpr -n run.ndx -rmcomm -beginfit 50000 -endfit > 400000 > > However, it often get killed for number of beads larger than 37, as shown > below: > > Reading file eqm.tpr, VERSION 4.0.3 (single precision) > Reading file eqm.tpr, VERSION 4.0.3 (single precision) > > Select a group to calculate mean squared displacement for: > Group 0 ( System) has 13042 elements > Group 1 ( PEO) has 37 elements > Group 2 ( WF) has 1301 elements > Group 3 ( W) has 11704 elements > Group 4 ( WF_W) has 13005 elements > Select a group: 1 > Selected 1: 'PEO' > > Now select a group for center of mass removal: > Group 0 ( System) has 13042 elements > Group 1 ( PEO) has 37 elements > Group 2 ( WF) has 1301 elements > Group 3 ( W) has 11704 elements > Group 4 ( WF_W) has 13005 elements > Select a group: 1 > Selected 1: 'PEO' > trn version: GMX_trn_file (single precision) > Reading frame 24000 time 240000.000 Killed. > > Is it also a bug in the program or have I done something wrong on the > command? > > Thank you! > > Best Regards > Yutian Yang > > > > -- > 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 > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
