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

loan.huynh at utoronto.ca loan.huynh at utoronto.ca
Tue Mar 10 21:55:23 CET 2009

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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