I forwarded your email to the GROMACS users list,
please use it for user questions. In this way you
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>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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