[gmx-users] Umbrella Sampling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Mar 31 19:25:21 CEST 2011

your comment:

which should be centred around 0.80nm

is flawed, as i mentioned earlier. also, it is not g_wham that is  
sensitive but the convergence and sampling of phase space that is  
sensitive. don`t remove any data. do evaluate your convergence.  
without convergence measures, a pmf is worse than useless.


-- original message --

Cheers Chris

If I remove the red histogram (the first of the wider distributions),
which should be centred around 0.80nm but is actually centred around
0.78 nm; and add in some more histograms with higher force constants the
profile changes slightly. It seems that  g_wham is very sensitive to
these subtleties. How do I know which curve is correct? I have about six
such curves that differ slightly in this manner.


chris.neale at utoronto.ca wrote:

[Hide Quoted Text]
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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