[gmx-users] Regarding calculating the water orientation profile

[soumadwip ghosh]

Hi Dilip,

Here is what you can do. In my guess, you are trying to calculate the
preferential binding affinity of water for N/C terminal domain of your
protein. You can look up for papers that contain Kirkwood-Buff integrals
and preferential binding coefficients. It basically works in the following
way:

1. Specify some atoms belonging to either N- or C-terminus (say COM or any
specific amino acid of your interest for each) and the OW atoms of SOL in
an index file. Calculate the RDF for OW from each separately. Say these
RDFs are g.n and g.c respectively. Now in the following equation

GN = integration (4*pi*r*r*(g.n-1)*dr) and CN = integration
(4*pi*r*r*(g.c-1)*dr )where . Take the integral value from zero till the
first solvation shell (say 3 angstrom, you can guess it from the RDF
profiles as well). Now calculate GN-CN. If its positive then water
molecules are preferentially bound to the N terminus or vice versa.

Let me know if you get it done. Best of luck!

Soumadwip Ghosh
Post Doctoral Research Associate
City of Hope National Medical Center
Duarte, CA 91010
United States