Simulation of cavitation bubble collapse

User discussions
1

GROMACS version: 2021
GROMACS modification: No
Here post your question:
Dear GROMACS users,
I’m trying to do a research on: molecular dynamics simulation on cavitation bubble collapse.
I know how to create a box and fill it with water.
what I don’t know is
1-how to create a bubble in the middle of the box ( by removing certain amount of water molecules)
2- how to add different molecules of gases, such as oxygen, nitrogen etc.

Could someone please provide me with the commands?

Thanks a lot,
Ali

2

For 1) I think that gmx select can give you all water molecules within or outside a radius of a given atom or molecule. You can then use that group in gmx editconf to get your water with cavity.
For 2) gmx insert-molecules will work if you make pdb or gro files with a gas molecule.