Invariant water molecules

User discussions
1

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 ?

2

Hi,
An option is to generate a dynamics selection using gmx select , gmx select — GROMACS 2021.1 documentation 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