Jianguo Li wrote:
Dear all,
I want to get the PMF of my peptide across the membrane bilayer. First I
pulled my peptide across the membrane and then did windowed umbrella
sampling along the reaction coordinates which is the z-distance between
peptide and membrane. However, I found that sampling is not sufficient
in some windows(e.g., around the center of the membrane). To enhance the
sampling, I am thinking to run the simulation in those windows at higher
temperature (e.g., 500K), but this will introduce a bias. My question
is: can g_wham remove the bias due to using different temperatures in
different windows?
If g_wham cannot deal with the bias due to using different T, I may need
to do REMD in those windows. But that will be very expensive
computationally. Anybody have an idea of enhancing sampling in those
windows?
Btw, I am using Martini CG model.
Any suggestions will be highly appreciated, thank you!
A more straightforward approach is to (1) add more sampling windows or (2)
increase the force constant in regions where there's poor sampling, or perhaps both.
-Justin
Cheers,
Jianguo
--
========================================
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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