Hi,
sorry for this late comment, I just stepped over this thread.
Bootstrapping is indeed slow, because a complete WHAM analysis must be
done for each bootstrap. I usually do much less bootstraps (around 50 to
100 gives a reasonable estimate), less bins, and I sometimes I reduce
the tolerance for convergence. I would first play a bit with the
tolerance and bins to see if they change your profile, probably they do
not. Then you can use, e.g.
-nBootstrap 100 -bins 200 -tol 1e-5
Cheers,
Jochen
Am 6/15/12 1:19 PM, schrieb Tsjerk Wassenaar:
Hey,
Most statistics texts on bootstrapping will advise taking in the order
of a thousand bootstrap samples. Don't know about the number of bins,
but in any case, the problem shouldn't be that hard computationally.
Have you checked the process? Is it really still running, has it
stalled? And how long does one bootstrap sample take to process?
Always good to check one before running a thousand...
Cheers,
Tsjerk
On Fri, Jun 15, 2012 at 12:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
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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