[gmx-users] Umbrella Sampling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Mar 31 18:36:12 CEST 2011

looks fine to me, no need to do that extra sampling that I suggested  
since it appears that you already did this -- benefits of seeing real  
data ;). If you want to understand why your histograms are not always  
centered at r0 (note that this is just fine) then you should read more  
about US, WHAM, and how to bias/debias the data for US (I am sure that  
there are textbooks around that explain this). The only case in which  
all of your histograms will be centered at their respective r0 is when  
the underlying PMF is exactly flat.


-- original message --

Hi Chris many thanks again for the advise. I have, or at least I thought
have sampled my barrier region to death, but as I say some histograms
may not be centred around r0. I will proceed with what you suggest.
Please find attached a picture of the histograms, the corresponding
profile, and a sample mdp file that I use.

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