[gmx-users] pull code and binding free energy

[Qasim Pars]

Dear users,

I was trying to do the binding free energy calculation between protein and
ligand. I get confused on the preparation of the input files:

First question: Why we need to use the pull code in the mdp files for the
binding free energy calculation (e.g.the pull code has used in this
tutorial:
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme)?
What does the pull code really do? I read the manual section 6.4 but it
didn't answer the questions in my head.

Second question: Instead of using the pull code in the mdp files, is it
better to use [ bonds ] under [ intermolecular-interactions ] in the
topology file?

Third question: The PMF or the binding free energy (alchemical) is the best
one to calculate free energy? And why?

Any answer will be greatly appreciated.

Cheers,

-- 
Qasim Pars