# Invariant water molecules

**URL:** <https://gromacs.bioexcel.eu/t/invariant-water-molecules/1671>\
**Category:** User discussions\
**Created:** [March 3, 2021, 5:25am UTC](https://gromacs.bioexcel.eu/t/invariant-water-molecules/1671 "2021-03-03T05:25:37Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![gromacsash](https://avatars.discourse-cdn.com/v4/letter/g/d6d6ee/32.png) [@gromacsash](https://gromacs.bioexcel.eu/u/gromacsash)\
**Post date:** [March 3, 2021, 5:25am UTC](https://gromacs.bioexcel.eu/t/invariant-water-molecules/1671/1 "2021-03-03T05:25:37Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question Dear all

I have run simulation for a protein (after removing all water from the structure) in water as medium.  
After simulation, I need only those water molecules at a distance of 5 angstrom units around it.  
That is, I need to reduce the number of water molecules so that I can use this for finding out the invariant waters around the protein.  
I also understand that during dynamics the protein as well as water keeps changing.  
Is there any tool in gromacs to directly calculate invariant water molecules ?

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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:** [March 9, 2021, 11:08am UTC](https://gromacs.bioexcel.eu/t/invariant-water-molecules/1671/2 "2021-03-09T11:08:11Z")

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Hi,  
An option is to generate a dynamics selection using gmx select , [gmx select — GROMACS 2021.1 documentation](https://manual.gromacs.org/current/onlinehelp/gmx-select.html) then analysis the results to see if some water molecules are always at 5 angstrom. Then you can analyze further to understand if they are bound or not to a specific pocket of the protein.

Maybe someone else has a better solution  
Best regards  
Alessandra