[gmx-users] Bootstrapping using g_wham

[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 <jalemkul at 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
>
> --
> ========================================
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands