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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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