[gmx-users] root-mean-square distance

dina dusti dinadusti at yahoo.com
Sun Jan 29 20:07:27 CET 2012

Hello Tsjerk,

Thank you from your reply, but in the many papers, radius of micelle has been obtained from both of them (i.e. gyration and root-mean-square distance from center of mass of micelle). I don't know that how should I compute the radius of a spherical micelle from rms distance of the headgroup atoms from the micelle center of mass. 

May I ask you to help me?

Best Regards

 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, January 29, 2012 2:02 PM
Subject: Re: [gmx-users] root-mean-square distance
Hi Dina,

g_rms calculates the RMS from pairwise distances after performing a
least-squares fit. That's quite different from what you want, and
actually is what you get from g_gyrate...



On Sun, Jan 29, 2012 at 8:09 AM, dina dusti <dinadusti at yahoo.com> wrote:
> Dear Specialists,
> I have a problem about computing of radius of micelle by
> root-mean-square-distance. Please help me.
> I obtained radius of my micelle 2.4 nm by g_gyrate.
> g_gyrate -f md.xtc -s md.tpr -o gyrate.xvg -b 150000
> I want compare it by rms distance.
> I use from g_rms as following:
> g_rms -f md.xtc -s md.tpr -o distrmsd.xvg -n index.ndx -b 150000
> It result me 3.992290e+00 nm after averaging by g_analyze -f distrmsd.xvg
> -av
> (the radius of a spherical micelle is defined as the rms distance of the
> headgroup atoms from the micelle center of mass, how should I define com of
> micelle in g_rms?)
> I think I am wrong somewhere.
> May I ask you to help me,Please?
> Best Regards
> Dina
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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