# How to center the complex after simulations?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-center-the-complex-after-simulations/2146>\
**Category:** User discussions\
**Created:** [May 11, 2021, 8:11pm UTC](https://gromacs.bioexcel.eu/t/how-to-center-the-complex-after-simulations/2146 "2021-05-11T20:11:52Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![amnah](https://avatars.discourse-cdn.com/v4/letter/a/8e7dd6/32.png) [@amnah](https://gromacs.bioexcel.eu/u/amnah)\
**Post date:** [May 11, 2021, 8:11pm UTC](https://gromacs.bioexcel.eu/t/how-to-center-the-complex-after-simulations/2146/1 "2021-05-11T20:11:52Z")

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GROMACS version:2020  
GROMACS modification: Yes/No  
Here post your question

I have run dynamic simulations for a complex that has (protein, DNA and RNA) . At the end of simulations, a small segment of the DNA is showing outside the box.  
I have used the following commands:  
1- gmx trjconv -f prodrun1.gro -s prodrun1.tpr -o prodrun\_nojump.gro -center -pbc nojump

2- gmx trjconv -f prodrun\_nojump.gro -s prodrun1.tpr -o prodrun1\_processed1.gro -center -pbc mol -ur compact  
3- gmx trjconv -s prodrun1.tpr -f prodrun1\_processed1.gro -o prodrun1\_processed1finalnew.gro -pbc mol -center

I have used the system (0) for both centering and for the output,

DNA segment is still oustide the box, How to center the whole complex before going for analysis?

Thank you so much

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**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:** [May 11, 2021, 8:22pm UTC](https://gromacs.bioexcel.eu/t/how-to-center-the-complex-after-simulations/2146/2 "2021-05-11T20:22:45Z")

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> [@amnah](#):
>
> I have used the system (0) for both centering and for the output,

Center on one species (the protein, the DNA, or the RNA) instead.

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<div class="post-metadata">

**Author:** ![amnah](https://avatars.discourse-cdn.com/v4/letter/a/8e7dd6/32.png) [@amnah](https://gromacs.bioexcel.eu/u/amnah)\
**Post date:** [May 11, 2021, 9:09pm UTC](https://gromacs.bioexcel.eu/t/how-to-center-the-complex-after-simulations/2146/3 "2021-05-11T21:09:03Z")

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> [@jalemkul](#):
>
> he protein, the DNA, or the RNA

I just tried that! but didn’t solve the problem