[gmx-users] root-mean-square distance

[dina dusti]

Hello Tsjerk,

Thank you very much, you're right, but I saw in several articles that had used from this for confirmation of results of gyration, or to obtain the radius of hydrocarbon core (by rms distance from the carbon bounded with head group to the micelle COM).
I also used from g_rmsdist, but it dose not have anything to determine center of mass of micelle.  


Best Regards
Dina


________________________________
 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 11:26 PM
Subject: Re: [gmx-users] root-mean-square distance
 
Hi Dina,

The radius of gyration is defined as sqrt( (1/N) tr X'(I-jj')X ),
which is the RMSD w.r.t. to the center of mass. It's the same thing.
But I was talking about the tools g_gyrate and g_rms. The latter fits
the structure to the reference structure and then sums the distances
between paired atoms. That only works if you have a reference with all
coordinates set to (0,0,0). But then the answer will be identical to
that of g_gyrate, so why bother? Use g_gyrate, because it does what
you want.

Cheers,

Tsjerk

On Sun, Jan 29, 2012 at 8:07 PM, dina dusti <dinadusti at yahoo.com> wrote:
> 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
> Dina
>
> ________________________________
> 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...
>
> Cheers,
>
> Tsjerk
>
> 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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-- 
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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