0. Thank you all who spent time answering my post (and especially for explanations how to convert bins into energy)! 1. Yes, force is 1000 kJ/mol/nm^2 in all windows 2. z is in nm as default in wham 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. Thank you once more! 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? Alex Alexander, please post the following: 1. force constants for your plot at http://picasaweb.google.ca/117558205101329348732/G_wham#5511287294315721970 NOTE: if they are all 1000 as in your first post, then you have a problem in your sampling. 2. units for your x-axis in the plot mentioned in part 1, above (i.e. angstroms or nanometers?) 3. convert one (only one) of your sampling probability histograms to an energy histogram and debias it (without using wham). To convert to energy, take each histogram bin and apply E=-kB*T*ln(P). Now debias by subtracting E_rest=0.5*Fc*(r-r0). You will have noise at each end, but what about the middle part, is it flat or not? Post a picture of this please. Chris Alexander Yakovenko Institute of Molecular Biology & Genetic of NAS of Ukraine 03143 acad.Zabolotnogo str. 150 Kiev Ukraine ______________________________________________ E-mail: yakovenk...@ukr.net
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