# Protein-protein interaction residues detection

**URL:** <https://gromacs.bioexcel.eu/t/protein-protein-interaction-residues-detection/480>\
**Category:** User discussions\
**Created:** [July 13, 2020, 10:46am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-residues-detection/480 "2020-07-13T10:46:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![darrenphua](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@darrenphua](https://gromacs.bioexcel.eu/u/darrenphua)\
**Post date:** [July 13, 2020, 10:46am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-residues-detection/480/1 "2020-07-13T10:46:18Z")

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For protein-protein aggregation or protein self-interaction simulations, can gromacs detect the residues that come into contact with each other over the trajectory?  
For example, over the trajectory, the proteins can ‘bump’ into each other or be in close proximity at multiple instances, and maybe by listing the most common interacting residues, one can label them as self-aggregation hotspots. Not sure if gromacs has such a function?

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**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\
**Post date:** [July 13, 2020, 11:21am UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-residues-detection/480/2 "2020-07-13T11:21:32Z")

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It’s worth looking through [http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#commands-by-name](http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#commands-by-name) to see what analysis GROMACS can perform.

For what you are looking to perform then [http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html](http://manual.gromacs.org/documentation/current/onlinehelp/gmx-distance.html) or [http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pairdist.html](http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pairdist.html) might be what you are after.

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**Author:** ![darrenphua](https://avatars.discourse-cdn.com/v4/letter/d/bcef8e/32.png) [@darrenphua](https://gromacs.bioexcel.eu/u/darrenphua)\
**Post date:** [July 13, 2020, 3:30pm UTC](https://gromacs.bioexcel.eu/t/protein-protein-interaction-residues-detection/480/3 "2020-07-13T15:30:41Z")

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Thanks for the links! Those are quite a lot of methods of analysis. Ill go through each one and try to pick the most suitable one for my work.