[gmx-users] Calculate asphericity of a group of atoms
suman at sscu.iisc.ernet.in
Tue Mar 10 23:34:53 CET 2009
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
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,
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