[gmx-users] pairwise rmsd

[Xavier Periole]

Kay Gottschalk wrote:

> Hi guys,
>
> I want to extract the two structures with the highest pairwise rmsd in 
> my simulation. I though g_rms -m should do the trick, but although 
> that gives a nice matrix, it's hard to extract the data from it. Any 
> ideas?
> Thanks,
> Kay.
>
You could use a PCA (g_covar) and then analyse it to extract the extreme 
conformations of
the first eigenvector (most dispersed structures along the first vector) 
using g_anaeig.
XAvier

-- 
----------------------------------------------

   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   Nijenborgh 4
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at rug.nl
   web-page: http://md.chem.rug.nl/~periole
   
----------------------------------------------