[gmx-users] trjconv -pbc nojump

Reisser, Sabine (IPC) sabine.reisser at kit.edu
Wed Sep 2 11:18:05 CEST 2015


I want to use trjconv -pbc nojump to create a trajectory without box jumping of molecules. The molecules (lipids) also start to diffuse out of the box like they should, but in some a part of the molecule still jumps (as I could observe in xy direction), while the rest doesn't, leading to artificially long bonds in VMD. I tried trjconv -pbc nojump both with a tpr file in the -s option, or a gro file (with only complete molecules), same result.

I'd be glad if somebody could give me a hint.



Dr. Sabine Reißer
Theoretical Chemical Biology
Institute of Physical Chemistry
Karlsruhe Institute of Technology

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