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

Suman Chakrabarty suman at sscu.iisc.ernet.in
Tue Mar 10 23:34:53 CET 2009

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.


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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.

Suman Chakrabarty
SSCU (Room # 106A)
Indian Institute of Science,
Bangalore, India.
PIN: 560012
Mobile: +91 98800 87948
            +1 607 342 4366
Homepage: http://www.namusite.com/

More information about the gromacs.org_gmx-users mailing list