[gmx-users] Bootstrapping using g_wham

[Justin A. Lemkul]

On 6/14/12 5:51 PM, rainy908 wrote:
> Hi,
>
> I am currently using bootstrapping in g_wham to estimate the uncertainty in my PMF.  I use a number of 1000 bootstraps.
>
> /software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \
>   -ip gwham.dat \
>   -bins 5000 \
>   -hist histo.xvg \
>   -bsres bsResult.xvg \
>   -nBootstrap 1000
>
> This process has been running on 1 node for the past 4 days straight, and I am not sure when it will ever finish.  Should I be concerned?
>

I certainly would be.  You're using a very large number of bins and bootstraps, 
far above the default value of 200 for each.  Do you need that many?  What 
happens if you run with values of 200 of -bins and -nBootstrap?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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