# How to analysis the MD result?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-analysis-the-md-result/9134>\
**Category:** User discussions\
**Created:** [May 12, 2024, 2:56am UTC](https://gromacs.bioexcel.eu/t/how-to-analysis-the-md-result/9134 "2024-05-12T02:56:28Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\
**Post date:** [May 12, 2024, 2:56am UTC](https://gromacs.bioexcel.eu/t/how-to-analysis-the-md-result/9134/1 "2024-05-12T02:56:29Z")

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GROMACS version:2022.2  
GROMACS modification: Yes/No  
Here post your question  
I did a Protein-ligand system and succeeded. Now I want to analysis the result, just like the frequency of interaction between a certain group of a small molecule and the relevant amino acids in a protein.  
Which command should I use? Or any free website?

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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:** [May 12, 2024, 2:42pm UTC](https://gromacs.bioexcel.eu/t/how-to-analysis-the-md-result/9134/2 "2024-05-12T14:42:45Z")

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I guess a good start would be to create an index file. `gmx make_ndx` and `gmx select` might be of use. Then you can use, e.g., `gmx distance` and `gmx hbond` for some analyses.