RE: PCA Analysis of CGMD

From: Rogan Carr (rogan_at_ks.uiuc.edu)
Date: Fri Apr 10 2009 - 09:47:35 CDT

Hi Anirban,

I just glanced through the source for g_covar, and it looks like you
should be able to use `g_covar' for any set of beads (not just CA
atoms). I think you specify the atoms/beads you want to use in an index
file with the `make_ndx' tool.

Cheers,
Rogan

On Fri, 2009-04-10 at 14:38 +0530, Anirban Ghosh wrote:
> Hello Josh,
>
>
>
> Thanks a lot for the reply. I think the Gromacs idea is a good one.
> But since I have a CG model with beads (and not amino acids), will it
> be possible to use g_covar (which calculates eigen vectors and
> eigen-values on the basis of C-alpha) to do this?
>
>
>
> Thanks,
>
>
>
>
>
> Anirban Ghosh
>
> Grade Based Engineer
>
> Bioinformatics Team
>
> Scientific & Engineering Computing Group
>
> Centre for Development of Advanced Computing
>
> Pune, India
>
>
>
>
> From:owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Joshua Adelman
> Sent: Thursday, April 09, 2009 8:58 PM
> To: Anirban Ghosh
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: PCA Analysis of CGMD
>
>
>
>
> 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.
>
>
>
>
>
> Josh
>
>
>
>
>
>
>
>
>
>
> 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
> http://nature.berkeley.edu/~jadelman
>
>
> Berkeley, CA 94720 USA jadelman_at_berkeley.edu
>
>
> ------------------------------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
>
>

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