battis...@libero.it wrote:
Dear all
I'd like to get the PMF using g_wham after umbrella sampling. I saw that PMF
profile dipend very strong from the windows selected in the z (reaction
coordinate) direction.
My idea is that the result of this method is much more qualitative than
quantitative. Are you in agreement with me?
No. The goal of WHAM is to calculate DeltaG. The method is quantitative.
My question is this. In the g_wham calculation, can I use two windows if I
have a "great exentended" overlap of z sampling into them?
Or is it necessary an overlap between adjacent windows, but no a so big
overlap?
The reliability of the PMF curve depends on the reliability of sampling. If
you're over-sampling in some regions along the reaction coordinate and
under-sampling in others, then the weighting is probably wrong and the result
inaccurate. I can't tell exactly from your description what's going on, but if
you have largely overlapping histograms, then your window spacing and/or force
constant settings are inappropriate.
-Justin
Thanks,
Anna
--
========================================
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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