[gmx-users] pull code and binding free energy

Qasim Pars qasimpars at gmail.com
Wed Nov 16 12:33:05 CET 2016

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
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.


Qasim Pars

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