[gmx-users] deltaG from PMF

Justin Lemkul jalemkul at vt.edu
Tue Aug 21 16:07:35 CEST 2012

On 8/21/12 9:36 AM, Steven Neumann wrote:
> Dear Gmx Users,
> I got confused about reading free energy difference from PMF curve.
> It is the difference between maximum value on PMF curve (plateau -
> final state) and the starting point corresponding to minima.
> So e.g. my curve starts at 0 [kcal/mol] going staright to minima of -2
> kcal/mol and then increase obtaining plateau of 14 kcal/mol. DeltaG =
> -16 kcal/mol or -12 kcal/mol ?

It seems that your system has discovered a more energetically favorable location 
where the minimum is at -2 kcal/mol.  It should not be assumed that whatever 
arbitrary "start" point we choose is the energy minimum.  In your case, it is 
not.  DeltaG is the difference between final and initial states.  Only you know 
what these states are.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list