Shahab,
Justin is entirely correct, you should read about potential of mean
force calculations, the gromacs pull code, and the gromacs free energy
code.
However, an important question is if you can *converge* the free
energy of macromolecular binding. If you don't know the bound state,
then I am sure that you can not. I think that it is even unlikely if
you do know the bound state.
I suggest that you start by calculating the Gibbs free energy of a
sodium ion binding to DNA. If you run the entire calculation in
duplicate, but starting from different configurations, you should get
a flavour of convergence difficulties and methods that you can apply
to enhance your convergence.
Chris.
shahab shariati wrote:
Hi gromacs users
Can I use gromacs for obtaining Gibbs free energy of binding of
protein and dna?
Yes. I would suggest you read about potential of mean force calculations.
-Justin
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