[gmx-users] a question about g_lie

[Jerry Song]

Hello, Dear gmx-users,



I have a question about g_lie.  I embedded a membrane protein-ligand complex in the lipid bilayer and performed the usual MD simulation.  I wish that I could use the resulting energy file to estimate the ligand binding affinity.  So the "solvents" here include the water, lipid bilayer and ion.  Then how can I calculate the Elj and Eqq at its unbound state?  



Can someone help me to clarify the procedure to calculate the linear interaction energy?   

Is the following steps right?



Perform the usual MD simulation the solvated protein-ligand complex 

Perform another MD simulation for free ligand and water. (If so, are there any specific requirements for the solvent system here? Do they have to be the same as the "solvent" system in the above step?) 

Calculate the average value of LJ and Coulomb interaction energies between free ligand and water as the input for Elj and Eqq



Thanks a lot!   



Jerry Song

Department of Chemistry

Rensselaer Polytechnic Institute
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