# Keep the two strands of DNA together **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [July 11, 2024, 4:03pm UTC](https://gromacs.bioexcel.eu/t/keep-the-two-strands-of-dna-together/9626 "2024-07-11T16:03:34Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![fatemeh](https://avatars.discourse-cdn.com/v4/letter/f/9de053/32.png) [@fatemeh](https://gromacs.bioexcel.eu/u/fatemeh)\ **Post date:** [July 11, 2024, 4:03pm UTC](https://gromacs.bioexcel.eu/t/keep-the-two-strands-of-dna-together/9626/1 "2024-07-11T16:03:34Z")
GROMACS version:2023.2 GROMACS modification: Yes/No I used `gmx trjconv` to correct for periodic boundary conditions (PBC) because the two strands of DNA separated during the simulation. I have a question: in the box containing DNA, water molecules, and ions, why was only one strand of DNA out of the box and water molecules and ions did not diffuse. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [July 12, 2024, 7:36am UTC](https://gromacs.bioexcel.eu/t/keep-the-two-strands-of-dna-together/9626/2 "2024-07-12T07:36:36Z")
Dear @fatemeh The box boundaries are virtual, everything diffuses around. Try something like `gmx trjconv -pbc none` on the whole system and you should be able to visualize the trajectory without PBCs. ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [July 13, 2024, 6:03pm UTC](https://gromacs.bioexcel.eu/t/keep-the-two-strands-of-dna-together/9626/4 "2024-07-13T18:03:13Z")
All the species diffuse around, so everything - eventually - will leave the simulation box. What do you mean with ‘only DNA is out of the box’?