# DNA chain abnormal in Molecular Dynamics simulation

**URL:** <https://gromacs.bioexcel.eu/t/dna-chain-abnormal-in-molecular-dynamics-simulation/9725>\
**Category:** User discussions\
**Created:** [July 24, 2024, 8:58am UTC](https://gromacs.bioexcel.eu/t/dna-chain-abnormal-in-molecular-dynamics-simulation/9725 "2024-07-24T08:58:25Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![pagumaaaaa](https://avatars.discourse-cdn.com/v4/letter/p/bc79bd/32.png) [@pagumaaaaa](https://gromacs.bioexcel.eu/u/pagumaaaaa)\
**Post date:** [July 24, 2024, 8:58am UTC](https://gromacs.bioexcel.eu/t/dna-chain-abnormal-in-molecular-dynamics-simulation/9725/1 "2024-07-24T08:58:25Z")

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GROMACS version: 2023.1-conda\_forge  
GROMACS modification: No

I want to learn the MD analysis of Protein and DNA interaction, and refer to the contents and methods in this article 《Directed-evolution mutations enhance DNA-Binding affinity and protein stability of the adenine base editor ABE8e》  
During the simulation, the entire cas9 DNA sgRNA complex was relatively stable in most of the time, but suddenly one of the double-stranded DNA moved to the outside of the complex and returned to the middle of the complex abnormally.  
The figure shows the RMSD of the complex as a whole, where the abnormal peak position corresponds to the abnormal movement of the DNA strand;  
 ![temp](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/b3ebf35a5b48335c02a81a3a7582d51a963d2c86.png)

What is the reason for this situation? Can you help me find a reasonable solution?

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<div class="post-metadata">

**Author:** ![pagumaaaaa](https://avatars.discourse-cdn.com/v4/letter/p/bc79bd/32.png) [@pagumaaaaa](https://gromacs.bioexcel.eu/u/pagumaaaaa)\
**Post date:** [July 24, 2024, 8:59am UTC](https://gromacs.bioexcel.eu/t/dna-chain-abnormal-in-molecular-dynamics-simulation/9725/2 "2024-07-24T08:59:43Z")

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![abnormal](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/8d890543aa206605c05bbd0a07a2cb6052f0cdb8.png)  
Here is the abnormal state pdb structure snapshot

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**Author:** ![al42and](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/al42and/32/1393_2.png) [@al42and](https://gromacs.bioexcel.eu/u/al42and)\
**Post date:** [July 24, 2024, 10:51am UTC](https://gromacs.bioexcel.eu/t/dna-chain-abnormal-in-molecular-dynamics-simulation/9725/3 "2024-07-24T10:51:18Z")

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Hi!

This is a common visualization/analysis issue (just search for “RMSD jump” or “RMSD fluctuation” on this forum) caused by the periodic boundary conditions.

You can use `gmx trjconv` to remove the jumps before analyzing your trajectory. Here you can find more details and the suggested workflow: [Terminology - GROMACS 2024.2 documentation](https://manual.gromacs.org/current/user-guide/terminology.html#periodic-boundary-conditions)

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<div class="post-metadata">

**Author:** ![pagumaaaaa](https://avatars.discourse-cdn.com/v4/letter/p/bc79bd/32.png) [@pagumaaaaa](https://gromacs.bioexcel.eu/u/pagumaaaaa)\
**Post date:** [August 8, 2024, 2:16am UTC](https://gromacs.bioexcel.eu/t/dna-chain-abnormal-in-molecular-dynamics-simulation/9725/4 "2024-08-08T02:16:59Z")

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Thank you so much!!  
I have referred to the method in the website you provided and processed my data according to the steps. Now I have got a track file with stable rmsd.

Thank you for your kind help!!