[gmx-users] Flat energy profile in g_wham

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Aug 30 21:53:52 CEST 2010

Alexander, please post the following:

1. force constants for your plot at  
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  


-- original message --

I don't know in advance which of them are redundant; moreover I am  
surprised if better scan of configuration space is something weird.  
Anyway I removed some windows (see histograms here  
and now PMF profile is 0.000000e+00 anywhere along z... Any ideas?

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"


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