[gmx-users] Free energy calculation
beneor at mail.ru
Thu Aug 2 16:07:42 CEST 2007
I need to calculate the free energy of complex formation between protein A and ligand B. I am about to simulate in solution the molecular dynamics of A, B and AB complex separately and calculate the free energy of each system using g_lie. Then, I suppose, deltaG = G(AB) - (G(A) + G(B)).
Is it a correct algorithm? Or maybe it's better to use "slow-growth" method (whith lambda = 1 for the absence of ligand in the binding pocket) to calculate the difference between G(AB) and G(A)?
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