[gmx-users] Free energy calculation

[Arneh Babakhani]

Why not do a steered MD or umbrella sampling, where you start with the
ligand in the binding pocket (in its correct conformation) and gradually
pull it out.  If done correctly, you should get a nice PMF.

> Hello!
> 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)?
> Thank you!
>
>
>
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