# How to calculate the number of hydrophobic interactions

**URL:** <https://gromacs.bioexcel.eu/t/how-to-calculate-the-number-of-hydrophobic-interactions/10187>\
**Category:** User discussions\
**Created:** [September 18, 2024, 10:10am UTC](https://gromacs.bioexcel.eu/t/how-to-calculate-the-number-of-hydrophobic-interactions/10187 "2024-09-18T10:10:44Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![sayan23us](https://avatars.discourse-cdn.com/v4/letter/s/65b543/32.png) [@sayan23us](https://gromacs.bioexcel.eu/u/sayan23us)\
**Post date:** [September 18, 2024, 10:10am UTC](https://gromacs.bioexcel.eu/t/how-to-calculate-the-number-of-hydrophobic-interactions/10187/1 "2024-09-18T10:10:44Z")

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GROMACS version:  
GROMACS modification: No  
How to calculate the number of hydrophobic interactions in a protein-ligand simulation performed in GROMACS?

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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:** [September 18, 2024, 10:49am UTC](https://gromacs.bioexcel.eu/t/how-to-calculate-the-number-of-hydrophobic-interactions/10187/2 "2024-09-18T10:49:04Z")

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Could you explain how you would count the number of hydrophobic interactions?

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**Author:** ![slovas](https://avatars.discourse-cdn.com/v4/letter/s/e274bd/32.png) [@slovas](https://gromacs.bioexcel.eu/u/slovas)\
**Post date:** [September 18, 2024, 2:12pm UTC](https://gromacs.bioexcel.eu/t/how-to-calculate-the-number-of-hydrophobic-interactions/10187/3 "2024-09-18T14:12:57Z")

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Strictly speaking there is no such thing as “hydrophobic” interaction. It is rather a hydrophobic effect, which is an entropy-driven process in protein folding.  
Nevertheless, you can check contact between hydrophobic side chains of amino acid residues and check for pi-pi, aromatic-amide, cation-pi and CH-pi interactions by determining from trajectories distances, angles etc. of such functions.

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**Author:** ![sayan23us](https://avatars.discourse-cdn.com/v4/letter/s/65b543/32.png) [@sayan23us](https://gromacs.bioexcel.eu/u/sayan23us)\
**Post date:** [September 20, 2024, 6:14am UTC](https://gromacs.bioexcel.eu/t/how-to-calculate-the-number-of-hydrophobic-interactions/10187/4 "2024-09-20T06:14:03Z")

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After docking of DNA and a druglike molecule , I have observed some hydrogen bonds and hydrophobic bonds(file attached ). After completion of md simulation I can calculate the hydrogen bonds, same way can I calculate hydrophobic bonds?  
 ![image.png](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/1c403ff201120a85711fb14333128b529ffda59b.png)

(Attachment sp.docx is missing)