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0. Thank you all who spent time answering my post (and especially for explanations how to convert bins into energy)!
<br />1. Yes, force is 1000 kJ/mol/nm^2 in all windows
<br />2. z is in nm as default in wham
<br />3. I made profile for w#10 (just in the case I attach forces file). the picture of window profile is there http://picasaweb.google.ca/117558205101329348732/G_wham#5511315785714749378.
<br />Thank you once more!
<br />P.S. Looks like (some of) you are not surprised with zeros in my wham output, but cant you please explain me what is wrong there?
<br />Alex
<br />
<br />
<blockquote class="ukr_editor_quotation" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">
<br />Alexander, please post the following:
<br />
<br />1. force constants for your plot at
<br />http://picasaweb.google.ca/117558205101329348732/G_wham#5511287294315721970
<br />NOTE: if they are all 1000 as in your first post, then you have a
<br />problem in your sampling.
<br />
<br />2. units for your x-axis in the plot mentioned in part 1, above (i.e.
<br />angstroms or nanometers?)
<br />
<br />3. convert one (only one) of your sampling probability histograms to
<br />an energy histogram and debias it (without using wham). To convert to
<br />energy, take each histogram bin and apply E=-kB*T*ln(P). Now debias by
<br />subtracting E_rest=0.5*Fc*(r-r0). You will have noise at each end, but
<br />what about the middle part, is it flat or not? Post a picture of this
<br />please.
<br />
<br />Chris
<br />
<br /></blockquote>
<br />
<br />Alexander Yakovenko
<br />Institute of Molecular Biology & Genetic of NAS of Ukraine
<br />03143
<br />acad.Zabolotnogo str. 150
<br />Kiev
<br />Ukraine
<br />______________________________________________
<br />E-mail: yakovenko_a@ukr.net
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