[gmx-users] entropy term in binding free energy calculation

sunyeping sunyeping at aliyun.com
Thu Dec 19 14:18:04 CET 2013

Dear all,
I am trying to calculate the entropy term of binding free energy using gromacs MD simulation. A strategy I can think of is: to do MD of the complex, the receptor and the ligand respectively and get the trajectories of the three species, and to calculate the entropy of the three species using g_anaeig, and then get the entropy change during the binding by the formula: delta (S) = S(complex)-S(ligand)-S(receptor). Is it a correct method for the purpose of calculating entropy contribution to the binding free energy? Or what is the correct way to calculte? Thanks in advance.
Yeping Sun
Institute of Microbiology, Chinese Academy of Sciences

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