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/
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