[gmx-users] umbrella curve

[Justin A. Lemkul]

parto haghighi wrote:
> Dear gmx users
> I have done umbrella sampling for a membrnae drug system and i have
> used 13 windows in this process but at last when I extracted the
> histogram curve I only had two peak.Is this reasonable?

No.  If you conducted 13 simulations, you should have 13 histograms, one for 
each window.  Perhaps you didn't plot the output correctly.

> Also  my PMF curve has several minimum and maximum points and at last
> it converges to zero.Is it true to report the difference of minimum
> and maximum points as the gibbs free energy value?

Recall that deltaG is a state function.  The final and initial states dictate 
the overall free energy change, not the path along which it evolves.  Different 
local minima and the magnitude of the barriers that separate them can be of 
interest, depending on the nature of the interactions occurring at those 
locations.  Be sure to conduct a thorough error analysis to be sure the 
magnitudes of the minima and maxima are actually significant.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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