How to calculate the number of interfacial water molecules?

User discussions
1

Hii all!

So I am studying protein DNA interactions. Can anyone guide me on how I can calculate the number of water molecules in the interface of protein and DNA?

Thank you!

2

Hi,
as far as I know there is not GMX tools doing this. But you could use gmx select (https://manual.gromacs.org/current/onlinehelp/gmx-select.html) to identify those molecules and write them a dynamic index.

Here you find the syntax for gmx select
https://manual.gromacs.org/current/onlinehelp/selections.html?highlight=selection

I hope it helps
Alessandra