[gmx-users] g_wham Error bars

Jochen Hub jhub at gwdg.de
Fri Feb 13 10:53:34 CET 2009

Raphael Alhadeff wrote:
> 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).

Hi Raphael,

there is a new g_wham available in the most recent gromacs version. It
is able to do bootstrapping. (check g_wham -h)

To get hopefully reliable error bars you need more umbrella histograms
and make sure that they are really independent. The new g_wham supports
bootstrapping of complete histograms (which are more
likely to be indpendet than consecutive simulations frames of one
umbrella window simulation.)

If you do bootstrapping from frames *within* one umbrella histograms you
will in some cases drastically underestimate the error because of hidden
long autocorrelations. Note that if you simulate a protein you most
often have long autocorrelations and it is difficult to estimate the
autocorrelation times.


Btw, if you encouter problems with the new g_wham please report them to
me. Thanks.

> Thanks in advance,
> Raphael
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Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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