[gmx-users] Energetics of ion and subatrate binding sites

[ram bio]

Dear Gromacs Users,

I have simulated a protein with different ions and same substrate bound to
it in POPC lipid bilayer using Groamcs 4.5.4. The ion binding and substrate
binding sites are coupled. After Md simulation we see a reorganization of
these sites. Now, we are trying to calculate the energetics of these ion
and substrate binding sites. Could any one please suggest  ideas or methods
to do the same in Gromacs package? Please let me know.

Thanks

Pramod