Re: Correlation matrix of the Ca atoms

From: Nicholas M Glykos (
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.


             Dr Nicholas M. Glykos, Department of Molecular 
         Biology and Genetics, Democritus University of Thrace,
   University Campus, 68100 Alexandroupolis, Greece, Fax +302551030613
      Tel ++302551030620 (77620),

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