[gmx-users] Free energy calculation

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 19 16:47:21 CEST 2008

Quoting shuai lu <luai.cpu at gmail.com>:

> Hello everyone,
> Here i want to caculate the binding free energy between an ligand and its
> receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part

Yes, among other things.  Read the manual regarding all the free energy options.
 Simply setting free_energy = yes will not be everything you need to consider.

> or use g_lie by doing  recepto-ligand-solvate md and ligand-solvate md
> separately?

g_lie will give you an estimate of free energy; I don't know how accurate it is
relative to a rigorous thermodynamic integration procedure.

> If run a md by set free_energy as "yes", how shoud i get free energy, just
> by g_energy alone or with some special parameter?

Check the mdrun output options (-dgdl)

> For anther method, can the energy calculated by  g_lie programme be thought
> as binding free energy?

Just as some general advice, search for Gromacs free energy tutorials.  There is
some good information on the wiki site, and there are some excellent tutorials
out there, most notably one written by David Mobley.  Many users have found
this tutorial to be very informative.


> Thank you!
> --
> Lu Shuai


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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