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.hu...@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-us...@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-requ...@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/ =================================== _______________________________________________ gmx-users mailing list gmx-users@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 the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
