# Using insert\_molecules command

**URL:** <https://gromacs.bioexcel.eu/t/using-insert-molecules-command/1499>\
**Category:** User discussions\
**Created:** [January 27, 2021, 9:49pm UTC](https://gromacs.bioexcel.eu/t/using-insert-molecules-command/1499 "2021-01-27T21:49:34Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ranarefaey](https://avatars.discourse-cdn.com/v4/letter/r/ba9def/32.png) [@ranarefaey](https://gromacs.bioexcel.eu/u/ranarefaey)\
**Post date:** [January 27, 2021, 9:49pm UTC](https://gromacs.bioexcel.eu/t/using-insert-molecules-command/1499/1 "2021-01-27T21:49:35Z")

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GROMACS version:2020.5  
GROMACS modification: No  
Here post your question Thank you for helping a novice out  
I am trying to insert a small molecule into a solvate bilipid layer using the command insert-molecules, but no molecules were added. I suspect it is because i need to use the -replace option. I want to know how do i specify the water molecules to replace.  
Thank you so much for your help

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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:** [January 29, 2021, 10:20am UTC](https://gromacs.bioexcel.eu/t/using-insert-molecules-command/1499/2 "2021-01-29T10:20:00Z")

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Hi,  
I understood that you want to insert a molecule in place of a specific water molecules.  
You can insert the molecule at specific position (specific of a water molecule) using the option of gmx insert-molecules `-ip` and delete the water molecule you want to replace  
or  
you can try to have use an index file with a group with only that specific water molecule as input to gmx insert-molecules together with the option -replace  
Maybe one this option works for your case  
Alessandra

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**Author:** ![ranarefaey](https://avatars.discourse-cdn.com/v4/letter/r/ba9def/32.png) [@ranarefaey](https://gromacs.bioexcel.eu/u/ranarefaey)\
**Post date:** [January 29, 2021, 10:38am UTC](https://gromacs.bioexcel.eu/t/using-insert-molecules-command/1499/3 "2021-01-29T10:38:36Z")

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Hi  
So i need to figure out which water molecules i need to replace and then specify those in the insert molecule command?