# How to obtain water cluster index file?

**URL:** <https://gromacs.bioexcel.eu/t/how-to-obtain-water-cluster-index-file/2039>\
**Category:** User discussions\
**Created:** [April 28, 2021, 6:43am UTC](https://gromacs.bioexcel.eu/t/how-to-obtain-water-cluster-index-file/2039 "2021-04-28T06:43:33Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![mj.rezayani](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/mj.rezayani/32/3918_2.png) [@mj.rezayani](https://gromacs.bioexcel.eu/u/mj.rezayani)\
**Post date:** [April 28, 2021, 6:43am UTC](https://gromacs.bioexcel.eu/t/how-to-obtain-water-cluster-index-file/2039/1 "2021-04-28T06:43:34Z")

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Dear all,

I want to analyze water cluster in my (polymer/water) system. Average number of clusters is 4. I want to know if it is possible to obtain index file for each cluster at a specific time? I want to distinguish them in vmd and I need index file of each water cluster.Gromacs just gave me maxclust.ndx.(maximum cluster size index)

Thank you in advance

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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:** [April 29, 2021, 12:49pm UTC](https://gromacs.bioexcel.eu/t/how-to-obtain-water-cluster-index-file/2039/2 "2021-04-29T12:49:38Z")

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Hi,  
a tools to generate dynamics index is gmx select.  
Here you find something on selection synthax  
[https://manual.gromacs.org/current/onlinehelp/selections.html?highlight=selection](https://manual.gromacs.org/current/onlinehelp/selections.html?highlight=selection)  
maybe it helps  
Best regards  
Alessandra