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

Yutian Yang yyang18 at syr.edu
Wed Jul 3 21:22:43 CEST 2013

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! 


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