# After simulation DNA double helix unwinding

**URL:** <https://gromacs.bioexcel.eu/t/after-simulation-dna-double-helix-unwinding/10557>\
**Category:** User discussions\
**Created:** [November 15, 2024, 12:47am UTC](https://gromacs.bioexcel.eu/t/after-simulation-dna-double-helix-unwinding/10557 "2024-11-15T00:47:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ummul](https://avatars.discourse-cdn.com/v4/letter/u/e9c0ed/32.png) [@ummul](https://gromacs.bioexcel.eu/u/ummul)\
**Post date:** [November 15, 2024, 12:47am UTC](https://gromacs.bioexcel.eu/t/after-simulation-dna-double-helix-unwinding/10557/1 "2024-11-15T00:47:18Z")

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GROMACS version:2022 and 2023  
GROMACS modification: Yes/No  
Here post your question  
hello all  
i want to discuss about why my dna double helical structure is unwinding after simulation  
i tried using different force fields like charmm36,charmm27, amber etc.,  
can you guys please suggest me what kind of mistake i am making.

i am adding the reference picture

 ![a_rmsd](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/aa5d4b0a2e1dd70af7bd6533dedebf2f84f4b01e.jpeg)

thanks in advance

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 15, 2024, 6:17am UTC](https://gromacs.bioexcel.eu/t/after-simulation-dna-double-helix-unwinding/10557/2 "2024-11-15T06:17:01Z")

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Do you base your statement that it is unwinding on the RMSD plot? That just looks like it’s crossing the PBC boundary. See if

```auto
gmx trjconv -f <trj_file.xtc> -s <topol.tpr> -o <output1.xtc> -pbc whole
gmx trjconv -f <output1.xtc> -s <topol.tpr> -o <output2.xtc> -pbc nojump

```

helps.  
See [Terminology - GROMACS 2024.4 documentation](https://manual.gromacs.org/current/user-guide/terminology.html#periodic-boundary-conditions) for more info.

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<div class="post-metadata">

**Author:** ![ummul](https://avatars.discourse-cdn.com/v4/letter/u/e9c0ed/32.png) [@ummul](https://gromacs.bioexcel.eu/u/ummul)\
**Post date:** [November 18, 2024, 12:48am UTC](https://gromacs.bioexcel.eu/t/after-simulation-dna-double-helix-unwinding/10557/3 "2024-11-18T00:48:17Z")

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Thank you for your response sir,  
yeah sir, Its crossing the PBC boundary, now i solved it sir.