Hi Yutian Yang, I don't think it's because of the size of the system. Can you run trjconv without -pbc nojump? And did you check the trajectory with gmxcheck? Does the output file exceed a maximum file size limit?
Hope it helps, Tsjerk On Wed, Jul 3, 2013 at 9:22 PM, Yutian Yang <yyan...@syr.edu> wrote: > Dear all, > > I want to remove PBC effects for my system and calculate the diffusion > coefficient. I am using Gromacs 4.5.4. My system is a 15 nm cubic box with > 376 polymer chains each with 28 beads. The simulation time is about 2000 > ns. However, when I use the command > > trjconv_mpi -f all.xtc -s polyeqm.gro -o allnojump.xtc -pbc nojump > > The program stops at around 500 ns. It doesn't get killed, nor proceeds, > but stuck there and I have to manually cease the program. I have tried > different systems with same attributes, all with the same problem. Is it > because it is a large system that makes the program running out of memory? > > Thank you! > > Yutian > > > > > > > > > > > > -- > 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
