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
Contact person: Fabio Lolicato (lolicato.fabio@gmail.com)
The tool has been tested for the following systems:
-
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 -
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