# DNA TOP file

**URL:** <https://gromacs.bioexcel.eu/t/dna-top-file/11067>\
**Category:** User discussions\
**Tags:** simulation-setup\
**Created:** [January 18, 2025, 6:02am UTC](https://gromacs.bioexcel.eu/t/dna-top-file/11067 "2025-01-18T06:02:00Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![mostafagh98](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mostafagh98/32/4214_2.png) [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\
**Post date:** [January 18, 2025, 6:02am UTC](https://gromacs.bioexcel.eu/t/dna-top-file/11067/1 "2025-01-18T06:02:00Z")

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GROMACS version: 2024  
GROMACS modification: No

Hi, I hope youre’doing well.

I am studying peptide/DNA interactions as well as DNA/membrane interactions using GROMACS. My DNA structure consists of two strands, and I am unsure whether to treat the DNA as a single molecule or as separate chains in my simulations.

Should I define the DNA as a single molecule in the topology file and use tools like `pdb2gmx -merge interactive` to merge the strands together? Or would it be better to treat the DNA strands as separate chains?

I want to ensure that I handle periodic boundary conditions correctly and avoid any broken molecule appearance in the trajectory. Which approach would be more appropriate for these types of simulations?

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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:** [January 24, 2025, 7:55pm UTC](https://gromacs.bioexcel.eu/t/dna-top-file/11067/2 "2025-01-24T19:55:35Z")

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hello,  
Hello,

The separation of two strands of DNA is because of PBC. If you consider a very, very, very big box, it is computationally expensive, and you will not see any separation. You can follow [my previous discussion](https://gromacs.bioexcel.eu/t/issue-with-correcting-pbc-for-dna-separation-in-gromacs/11013) for the correction of two separate DNA strands. Putting them in an ITP is useful when you want to apply a restraint to DNA, which must be in one ITP. Furthermore, if there is a covalent bond between DNA and protein, you must merge the ITP.

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**Author:** ![mostafagh98](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mostafagh98/32/4214_2.png) [@mostafagh98](https://gromacs.bioexcel.eu/u/mostafagh98)\
**Post date:** [January 27, 2025, 5:48pm UTC](https://gromacs.bioexcel.eu/t/dna-top-file/11067/3 "2025-01-27T17:48:20Z")

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Thank you so much for your response!