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.
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