[gmx-users] protein+2water molecules

[Dmitry Kovalsky]

Hi All,
Is it possible while converting trajectory from trr to xtc (or any other format, using trjconv)  to obtain protein plus few water molecules which are of my interest. I mean that there are 2 water molecules in active site which trajectory is important for me and I want to see them in my trajectory after removing the bulk solvent molecules. Or another way like this: to create a sphere with definable center and radius (for example with its center  in the center of active site). All solvent molecules which are within the shpere become visible in converted trajectory. 

Cheers,
Dmitry