[gmx-users] monitoring the water molecules

[Mark Abraham]

On 17/06/2011 12:55 PM, Ramachandran G wrote:
> 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

They have the same atom number throughout. Whatever you want to do can 
be done using them, possibly via g_select creating dynamic selection groups.

Mark