Re: Correlation matrix of the Ca atoms

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Mon Feb 02 2009 - 02:17:39 CST

> I want to calculate the Correlation matrix of the Ca atoms (motion) in
> a 5 ns simulation done on NAMD, so that the relationship of the
> residual and domain motion can be found out.

You can use carma directly with your dcd-psf with a one-liner:

     # carma -v -w -col -cov -dot -norm protein.dcd protein.psf

should do the trick.

Nicholas

-- 
             Dr Nicholas M. Glykos, Department of Molecular 
         Biology and Genetics, Democritus University of Thrace,
   University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
      Tel ++302551030620 (77620),  http://www.mbg.duth.gr/~glykos/

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:27 CST