Re: [gmx-users] unwrap trajectory file using -pbc nojump

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 wrote: > De

[gmx-users] unwrap trajectory file using -pbc nojump

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