RE: PCA Analysis of CGMD

From: Anirban Ghosh (anirbang_at_cdac.in)
Date: Fri Apr 10 2009 - 04:08:25 CDT

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

 

 

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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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