[gmx-users] radius of gyration

[Justin A. Lemkul]

On 5/8/12 4:08 PM, dina dusti wrote:
> Dear Justin,
>
> Thank you very much from your help.
> Yes, the micelle was created after 100 ns from start of simulation.
> If the first procedure is true, so why the error estimate is so small and why
> the error estimate of Rg is so different with Rg(x,y,z)?
>

For the algorithmic specifics of how the error estimate is calculated, refer to 
Berk's paper.

The error estimate is smaller in the case of starting after 100 ns because in 
the case where you consider all the data, you are calculating Rg of diffuse 
molecules and a micelle.  You're considering two different states and thus your 
data are poorly converged with respect to that measurement.

-Justin

-- 
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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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