Re: PCA Analysis of CGMD

From: Joshua Adelman (
Date: Thu Apr 09 2009 - 10:28:06 CDT

Hi Anirban,

There are a lot of options out there for doing this from writing your
own code (for example using the MatDCD package to load the coordinates
into matlab), or using a number of other available packages. The way I
like to do it is to use catdcd to convert my trajectories into .trr
format and then use the tools available in Gromacs (g_covar to
calculate the eigenval/vecs and g_anaeig to project the trajectories
onto particular modes and to generate pdb files to visualize them), to
do PCA.


On Apr 9, 2009, at 5:23 AM, Anirban Ghosh wrote:

> Hi ALL,
> I have done a CGMD simulation of a three chain protein system using
> NAMD. Is it possible to do a Principle Component Analysis (PCA) of
> this CGMD run? If yes, then how? Any suggestion is welcome.
> Regards,
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Scientific & Engineering Computing Group
> Centre for Development of Advanced Computing
> Pune, India

Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley
Berkeley, CA 94720 USA

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