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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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