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
--
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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