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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
