[gmx-users] Re: Re: Flat energy profile in g_wha

[Justin A. Lemkul]

alexander yakovenko wrote:
>   Sorry for poor explanations.
> My histogram is here http://picasawe b.google.ca/117 558205101329348 
> 732/G_wham#5511 244561053627250 
> <http://picasaweb.google.ca/117558205101329348732/G_wham#5511244561053627250> 
> it was 12 ns per window run.

Looks to me like your windows overlap too much - there is complete redundancy in 
many of them, such that it looks like several of your windows are completely 
unnecessary.  See the example histogram in the PMF tutorial for a more "normal" 
histogram.

-Justin

> Regards,
> Alex.
> 
>  
> 
>     alexander yakovenko wrote:
>      > Hi Justin!
>      > Thank you for replay. My histogram (can send if required)
>     consists of 13
>      > windows (0.1 and 0.2nm sampling) and look like two peaks (with
>      > amplitudes 3-4e+2) separated with a valley of 1.2-1.5e+2 (my
>     protein has
>      > two sub-domains so should be OK) and smallest overlap between
>     windows is
> 
>     I don't understand this description. How can 13 windows produce only
>     two peaks?
> 
> 

-- 
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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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