Hello,
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
deviation
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,
Nicolas
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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