Re: Correlation matrix of the Ca atoms

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Sun Feb 01 2009 - 23:22:07 CST

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?
> 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
>

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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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