[gmx-users] g_wham PMF profile

[Justin A. Lemkul]

battistia at 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
> 

-- 
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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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