[gmx-users] Calculate asphericity of a group of atoms

[Suman Chakrabarty]

Hi Loan,

you could calculate the radii of gyration about the principal axes
using the "-p" option of the analysis program "g_gyrate".

The ratio of the largest and smallest eigenvalues (essentially the
radii of gyration along the principal axes) could serve as an
"asphericity" index.


Regards,
Suman.


On Tue, Mar 10, 2009 at 4:55 PM,  <loan.huynh at utoronto.ca> wrote:
> Hi everyone,
>
> I would like to measure the asphericity of a group of atoms.  Base on
> literature searching results, there are studies measure the asphericity
> using the radius of gyration tensor, compute the eigenvalues of this tensor,
> and use these eigenvalues to compute asphericity (0<=delta =<1) (e.g., H. T.
> Tran, Biophysical Journal, 91, 2006 1868).
>
> I?m wondering if anyone has done this before using the radius of gyration?
>
> From my understanding, by using the g_gyration in Gromacs, I can receive Rg
> and radius of the gyration about x, y, z axis (Rx, Ry, Rz) where Rg =
> sqrt((Rx^2 + Ry^2 + Rz^2)*0.5).
> Also, with the option ?moi, I get the moments of inertia Itot, I1, I2, I2,
> where Itot= sqrt(I1+I2+I3), and I = mass*Rg^2
>
> Is it possible to calculate the eigenvalues base on Rg or I values?
>
> Any input is greatly appreciate,
>
> Thanks,
> Loan
>
>
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