# Utilizing GROMACS Simulation Files for DNA Structure Analysis with the biobb\_dna Package

**URL:** https://ask.bioexcel.eu/t/utilizing-gromacs-simulation-files-for-dna-structure-analysis-with-the-biobb-dna-package/5003
**Category:** BioBB
**Tags:** gromacs
**Created:** [May 13, 2024, 3:20pm UTC](https://ask.bioexcel.eu/t/utilizing-gromacs-simulation-files-for-dna-structure-analysis-with-the-biobb-dna-package/5003 "2024-05-13T15:20:53Z")
**Posts on this page:** 1
**Showing post:** 12

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### Author: ![adam.hospital](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/adam.hospital/32/151_2.png) [@adam.hospital](https://ask.bioexcel.eu/u/adam.hospital)
#### Post date: [August 19, 2024, 10:41am UTC](https://ask.bioexcel.eu/t/utilizing-gromacs-simulation-files-for-dna-structure-analysis-with-the-biobb-dna-package/5003/12 "2024-08-19T10:41:46Z")

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Hi Fatemeh,

[response cloned from a previous [post](https://ask.bioexcel.eu/t/exploring-the-limitations-of-biobb-dna-in-handling-large-dna-sequences/5017/4)]

it is difficult to find the reasons of this without the trajectory file. I guess the quality check analyses (RMSd, fluctuation, HBs, etc.) are not giving any strange jumps, is that right? If so, could you please try to share the topology and trajectory files with me somehow? Maybe with an on-line file sharing service like Google drive? (I know they are big)

Looking forward to your reply.

Regards,

-Adam-

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