[gmx-users] radius of gyration

dina dusti dinadusti at yahoo.com
Tue May 8 22:50:51 CEST 2012

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

 From: Justin A. Lemkul <jalemkul at vt.edu>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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 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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