[gmx-users] Analysis the dynamics of water molecules

[Soham Sarkar]

Hello,
    I have a 200ns trajectory of protein-water-urea mixture, saved at 2ps
interval. I want to calculate the angle distribution of water molecule
(<O-O-O angle distribution) like represented under Figure. 2 of the paper
'J. Phys. Chem. B, Vol. 114, No. 10, 2010' by Jana and Bagchi. They have
calculated the <O-O-O angle distribution at the minor, major groove also in
the bulk water. I want to calculate that angle distribution near the
helices region of the protein and at the bulk water. Could anyone please
provide me with the procedure that I should follow to execute that analysis?
 Thanks in advance-
Soham