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
