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

[alexander yakovenko]

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: yakovenko_a at ukr.net
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100831/16ca4ef2/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: pullf_u10.xvg.bz2
Type: application/octet-stream
Size: 32945 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100831/16ca4ef2/attachment.obj>