Dear Justin,
Thank you very much from your help, but may I ask you to say me why the error
estimate of Rg is very smaller than Rgx, Rgy, Rgz, Please? I didn't understand
any thing from paper about this problem!
Best Regards
Dina
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: dina dusti <dinadu...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Wednesday, May 9, 2012 12:44 AM
Subject: Re: [gmx-users] radius of gyration
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
-- ========================================
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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