**From:** Joshua Adelman (*jadelman_at_berkeley.edu*)

**Date:** Sun Feb 01 2009 - 23:22:07 CST

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I find that the easiest way to do this is to download and compile the

tools that come with gromacs (http://www.gromacs.org/) and use g_covar

and g_anaeig to analyze the principal components. You can also write

out the covariance matrix, and I believe there is also a variation of

g_covar in the user contributed software that calculates the

correlation matrix directly. There is probably other software out

there, but gromacs has a lot of nice tools all in one place.

You will have to convert your dcd file to trr, which is pretty easy

using catdcd.

Josh

On Feb 1, 2009, at 8:46 PM, sripad chandan wrote:

*> Friends,
*

*> 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.
*

*> Is there any possibility of doing it by NAMD/VMD?
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*> It will be very helpful if some one can give a suggestion atleast.
*

*> Thanks alot.
*

*> Chandan
*

*>
*

*>
*

*> --
*

*> Sripad Chandan Patnaik
*

*> Research Assistant
*

*> National Institute of Technology, Rourkela
*

*> +91-9861668977
*

*>
*

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

Joshua L. Adelman

Biophysics Graduate Group Lab: 510.643.2159

218 Wellman Hall Fax: 510.642.7428

University of California, Berkeley http://nature.berkeley.edu/~jadelman

Berkeley, CA 94720 USA jadelman_at_berkeley.edu

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