I forwarded your email to the GROMACS users list,
please use it for user questions. In this way you
have a greater chance of getting answers and others
can find the questions and answers online.

>I have a 2 microsecond trajectory of protein-ligand system. I want to 
>calculate 3 things:
>1. Time series of number of water molecules in binding cavity.

Give gmx select a try. You could select water molecules within
a certain distance of atoms of cavity lining residues.

>2. Volume evolution of in the binding cavity.

There are a number of tools not distributed with GROMACS
that you could try, for example
and caver https://www.caver.cz

>3. Water surface density evolution in the cavity.

I'm not sure how you would define this quantity
but a combination of the select and sasa tools of
gmx may work.


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