[gmx-users] Number of windows in umbrella sampling

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 14 15:05:21 CET 2012

Justin A. Lemkul wrote:
> shahid nayeem wrote:
>> Thanks Justin. I will try again. But please refer to some protocol if 
>> you know and one last question that before doing umbrella sampling 
>> simulation how can one be sure that the pulling is good and one should 
>> go ahead with selecting window and doing umbrella sampling. In the end 
>> when you see histo.xvg and profile.xvg , it cost a lot computationally 
>> and if you  don't get it right these computational resources are wasted. 
> There are certainly simulations that have been published using umbrella 
> sampling on a variety of systems.  I'm sure some relatively quick 
> literature searching will lead you to some suitable ideas.  Spending a 
> few hours doing some reading will save you months of wasted CPU time.

I should, of course, mention that what you have done is not necessarily wasted, 
it's simply insufficient.  Simulations can always be extended and new umbrella 
sampling windows added after the fact and incorporated into the analysis.  A 
better experimental plan will save these headaches in the future.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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