# Pbc effect removal

**URL:** <https://gromacs.bioexcel.eu/t/pbc-effect-removal/1132>\
**Category:** User discussions\
**Created:** [November 20, 2020, 8:45pm UTC](https://gromacs.bioexcel.eu/t/pbc-effect-removal/1132 "2020-11-20T20:45:21Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [November 23, 2020, 9:58am UTC](https://gromacs.bioexcel.eu/t/pbc-effect-removal/1132/2 "2020-11-23T09:58:42Z")

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Hi,  
This topic has been addressed several times in the forum. Maybe you find the answer already in the forum using the option search.

Maybe the answer to this post can help

> [@Seemingly unresolvable PBC problem on protein complex](https://gromacs.bioexcel.eu/t/seemingly-unresolvable-pbc-problem-on-protein-complex/786):
>
> GROMACS version: 2019.4 GROMACS modification: No Dear All, I have a protein complex on which I ran some REMD and I want to solve PBC issues before analysis. However, no matter what I tried, one of the proteins still jumps out of the box. Firstly I make the system whole with: $gmx trjconv -f md.xtc -s nvt\_298.15.tpr -pbc whole -o whole -n index.ndx This makes the molecules whole, although both proteins in the complex “jump around”. I have then centered the system on an interfacial residue…

Best regards  
Alessandra

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