[gmx-users] g_wham Error bars

Nicolas nsapay at ucalgary.ca
Fri Feb 13 03:54:05 CET 2009


As far as I know, it is not possible to directly calculate and error bar 
with g_wham . At that point, you've got several options:

    1) You can run several times your umbrella sampling simulations,
    calculate several PMFs,  then calculate an average and a standard
    2) if your simulations are split in several parts, you can calculate
    a PMF for each part and check their convergence over the time.
    3) if your PMF is supposed to be symmetrical, you can mirror it,
    calculate the difference between the PMF and its image, then used
    the difference/2 as a rough estimate of the error.

Hope that helps,

Raphael Alhadeff a écrit :
> Hello everyone,
> I wanted to ask if anyone knows how to compute standard deviation, for 
> the sake of adding error bars to an energy profile output using g_wham 
> (PMF using umbrella sampling in my case).
> Just to clarify, I am talking about the deviation of the energy 
> profile on ONE simulation (composed of 25 "windows" in my case, with 
> overlap but no repeats).
> Thanks in advance,
> Raphael
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