# sol\_remover

**URL:** <https://gromacs.bioexcel.eu/t/sol-remover/909>\
**Category:** Third party tools and files\
**Created:** [October 5, 2020, 8:42am UTC](https://gromacs.bioexcel.eu/t/sol-remover/909 "2020-10-05T08:42:36Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![fabiolol](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/fabiolol/32/399_2.png) [@fabiolol](https://gromacs.bioexcel.eu/u/fabiolol)\
**Post date:** [October 5, 2020, 8:42am UTC](https://gromacs.bioexcel.eu/t/sol-remover/909/1 "2020-10-05T08:42:36Z")

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sol\_remover is a Python script that removes all the specified residues from the given .gro file that are in a specific range.  
The intended use is to remove water molecules from the inside of the membrane.  
This is done by calculating the average of the z components of the specified atom both for the upper and the lower leaflet.  
All the water molecules that are between the leaflets are then removed.

If the option -p is specified, the .top file is updated automatically.

Link: [https://gitlab.com/fabiolol/sol\_remover](https://gitlab.com/fabiolol/sol_remover)  
Contact person: Fabio Lolicato ([lolicato.fabio@gmail.com](mailto:lolicato.fabio@gmail.com))

The tool has been tested for the following systems:

1. For Martini systems:  
sol\_remover -f solv.gro -o solv\_fix.gro --rn W --ra W --rs 1 --ln POPC --la PO4 -p topol.top

2. For All atoms systems:  
sol\_remover -f solv.gro -o solv\_fix.gro --rn SOL --ra OW --rs 3 --ln POPC --la P -p topol.top