# Fix two separate DNA strands after simulation using -pbc cluster

**URL:** <https://gromacs.bioexcel.eu/t/fix-two-separate-dna-strands-after-simulation-using-pbc-cluster/9704>\
**Category:** User discussions\
**Tags:** pbc, analysis-tools\
**Created:** [July 22, 2024, 10:14am UTC](https://gromacs.bioexcel.eu/t/fix-two-separate-dna-strands-after-simulation-using-pbc-cluster/9704 "2024-07-22T10:14:50Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![fatemeh](https://avatars.discourse-cdn.com/v4/letter/f/9de053/32.png) [@fatemeh](https://gromacs.bioexcel.eu/u/fatemeh)\
**Post date:** [July 22, 2024, 10:14am UTC](https://gromacs.bioexcel.eu/t/fix-two-separate-dna-strands-after-simulation-using-pbc-cluster/9704/1 "2024-07-22T10:14:51Z")

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GROMACS version:2023.2  
GROMACS modification: Yes/No  
Here post your question

hello,  
I have used these two commands to fix two separate DNA strands.  
gmx trjconv -f file.xtc -s file.tpr -pbc cluster -o file-cluster.xtc  
gmx trjconv -f file-cluster.xtc -s file.tpr -pbc mol -center -o file-cluster\_center.xtc

and for further visualization i used file-cluster\_center.xtc. in the system i have only DNA , water molecules and ions for notarization. is it correct? do I miss any information?