[gmx-users] Bootstrapping using g_wham
Justin A. Lemkul
jalemkul at vt.edu
Fri Jun 15 12:35:22 CEST 2012
On 6/14/12 5:51 PM, rainy908 wrote:
> 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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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