[gmx-users] deltaG from PMF

[Steven Neumann]

On Tue, Aug 21, 2012 at 3:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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

Thank you. Ok - mu curve starts at 0 kcal/mol corresponding to the
reaction coordinate of 0.5 nm. going to -2 kcal mol at 0.6 nm then
increasing as I said before to plateau of 14 kcal/mol.

My first window (shown by grompp) corresponds to 0.8 nm of the
reaction coordinate... So the initial state should be at 0.8 nm which
corresponds to 0.5 kcal/mol or always take the initial state as
initial of the curve?

Sorry, got confused.

Steven


>
> --
> ========================================
>
> 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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