[gmx-users] water handling

[Ken Rotondi]

Hello,

I've run some trajectories in explicit solvent. I'd like to observe the 
behavior of the water molecules in the first several layers of solvent 
around the protein. Is there any way in the GROMACS package that I can 
strip away the bulk water and look at snapshots of just the protein and 
its associated waters? I've looked through trjconv but did not see a 
solution to my need.

As always, thanks in advance for any help,

Ken

K.S.Rotondi
Research Associate
The Gierasch Laboratory
The University of Massachusetts-Amherst