[gmx-users] monitoring the water molecules

[Ramachandran G]

Hi gmx-users.
    I am doing MD simulation with the green fluorescent protein, where
confined water molecules exist inside the protein barrel.
During the coarse of the simulation i noticed these confined water molecule
get exchange with outside bulk water.

Is it possible to monitor or mark the water molecules during the
simulations? For my analysis it would be very much useful.
Can anyone guide me? Thanks

Rama
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