# Pbc nojump not working? **URL:** \ **Category:** User discussions\ **Created:** [December 31, 2020, 11:18pm UTC](https://gromacs.bioexcel.eu/t/pbc-nojump-not-working/1365 "2020-12-31T23:18:34Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![kwaldner](https://avatars.discourse-cdn.com/v4/letter/k/ecc23a/32.png) [@kwaldner](https://gromacs.bioexcel.eu/u/kwaldner)\ **Post date:** [December 31, 2020, 11:18pm UTC](https://gromacs.bioexcel.eu/t/pbc-nojump-not-working/1365/1 "2020-12-31T23:18:34Z")
Hello everyone, I have a gro file from an equilibration run of my protein. When I opened this using VMD, parts of the protein have moved out of the water box. I tried the following command to move the protein back into the water box as follows, gmx trjconv -f equilibration.gro -s equilibration.tpr -o equilibration\_pbc.gro -pbc nojump However, the new gro file still looks the same as the old one. Am I doing something wrong? Also, does this have anything to do with comm-grps or compressed-x grps/energygrps? I left them empty in the mdp file. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 1, 2021, 1:19am UTC](https://gromacs.bioexcel.eu/t/pbc-nojump-not-working/1365/2 "2021-01-01T01:19:18Z")
You should make molecules whole before removing jumps. > **[Terminology — GROMACS 2020.4 documentation](https://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow)** ---
**Author:** ![kwaldner](https://avatars.discourse-cdn.com/v4/letter/k/ecc23a/32.png) [@kwaldner](https://gromacs.bioexcel.eu/u/kwaldner)\ **Post date:** [January 1, 2021, 2:48am UTC](https://gromacs.bioexcel.eu/t/pbc-nojump-not-working/1365/3 "2021-01-01T02:48:18Z")
> [@kwaldner](#): > > gmx trjconv -f equilibration.gro -s equilibration.tpr -o equilibration\_pbc.gro -pbc nojump Thanks! For users who are facing something similar, I found this to be really helpful, 1 - To make broken molecules whole: gmx trjconv -f output.gro -s system.tpr -o new1.gro -pbc whole – Select the whole system - group 0 2 - Check if atoms jump across the box and put them back into the box: gmx trjconv -f new1.gro -s system.tpr -o new2.gro -pbc nojump – Select the whole system - group 0 3 - Cluster all the atoms in a specific chosen group, and center the system in the box: gmx trjconv -f new2.gro -s system.tpr -o new3.gro -pbc cluster -center yes – Select the the solid for the clustering and the centering, then select the system for output. [https://www.researchgate.net/post/How-to-remove-GROMACS-periodic-boundary-conditions](https://www.researchgate.net/post/How-to-remove-GROMACS-periodic-boundary-conditions)