[gmx-users] Re: question about free energy. Gromacs user

Arneh Babakhani ababakha at mccammon.ucsd.edu
Thu Aug 9 21:32:55 CEST 2007

> Maybe it should be obvious, but (a) why are you constraining two
> distances, and (b) are you sure your constraints aren't going to muck
> with the internal degrees of freedom for the ligand? I would think one
> would like to pull the ligand out of the receptor along some
> particular direction, but without doing anything to alter its internal
> degrees of freedom, or there would be a free energy associated with
> changing its internal degrees of freedom that you wouldn't capture in
> the PMF calculation.

I agree with David's comments here.  Check out the 'Special Topic' section
of the GMX manual.   you can either do a pulling simulation or umbrella
sampling (where the position and constrain the ligand on some rxn
coordinate, in several simulation).  The output of such simulatsions is a
*.pdo file, which you can then run g_wham on to obtain a PMF.

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