# Calculating complexation ion interactions

**URL:** <https://gromacs.bioexcel.eu/t/calculating-complexation-ion-interactions/2830>\
**Category:** User discussions\
**Tags:** analysis-tools\
**Created:** [September 19, 2021, 3:44pm UTC](https://gromacs.bioexcel.eu/t/calculating-complexation-ion-interactions/2830 "2021-09-19T15:44:28Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![gonzaloqe](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/gonzaloqe/32/653_2.png) [@gonzaloqe](https://gromacs.bioexcel.eu/u/gonzaloqe)\
**Post date:** [September 19, 2021, 3:44pm UTC](https://gromacs.bioexcel.eu/t/calculating-complexation-ion-interactions/2830/1 "2021-09-19T15:44:28Z")

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GROMACS version: 2020.3  
GROMACS modification: No

Hello dear community,

I have been studying the interaction between polymers with surfaces. Generally, this occurs mediated by an ion in a surface — ion — polymer form, where it is counted as interaction when the ion is interacting with the surface and the polymer simultaneously.

I use my own program to determine the amount of these interactions over time, but it is quite slow because the surface and polymers have several actives sites to interact.

I wonder if there is a way to do it with the Gromacs analysis programs to count these interactions. Unfortunately the gmx mindist program can only determine pair interactions I think.

Kind regards

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**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\
**Post date:** [September 22, 2021, 8:29am UTC](https://gromacs.bioexcel.eu/t/calculating-complexation-ion-interactions/2830/2 "2021-09-22T08:29:35Z")

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Hi,  
maybe gmx mindist together with option -on (number of contact) and -d (0.6) distance for contacts, and -ng (1) number of secondary groups to compute distance to a central group, can provide information that with a small analysis are in the direction

Or if you have already a code, maybe you can use analysis template (gromacs-202X.X/share/template/template.cpp) to build you on tools.  
Here you can find some documentiation on [Gromacs: Framework for trajectory analysis](https://manual.gromacs.org/current/doxygen/html-lib/page_analysisframework.xhtml)

Best regards  
Alessandra