[gmx-users] root-mean-square distance

[Tsjerk Wassenaar]

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