[gmx-users] g_anaeig

T.A.Wassenaar T.A.Wassenaar at rug.nl
Fri Mar 25 08:54:38 CET 2005

Hi Narender,

To get what you want, you would actually have to construct 
the covariance matrix for residues rather than atoms, and 
use that for further ED. However, to get close to that, 
you can do the ED on c-alpha atoms, as it has been shown 
by Andrea Amadei (forgot the reference) that there usually 
isn't any big difference between the motions of the 
c-alpha atoms and the rest of the residue.

Hope it helps,


On Thu, 24 Mar 2005 13:54:06 -0500
  "narender maan" <nsmaan at hotmail.com> wrote:
> Dear gmx-users I am doing ED of my simulation and while 
>using g_anaeig the file (eigrmsf.xvg) i am getting for 
>rmsf (by using -rmsf option) is for all the atoms in the 
>protein. So i was wondering if there's anyway to 
>calculate averages for each residue in eigrmsf.xvg 
>instead of atoms (like the way it is in g_rmsf by using 
>the option of -res)   thank you NSM  

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