Re: PCA calculation

From: NAVEEN P MICHAUD AGRAWAL (nmichaud_at_jhu.edu)
Date: Mon Feb 11 2008 - 11:58:34 CST

*Real* programmers use python and numpy ;)

You can use MDanalysis (mdanalysis.googlecode.com). There is even a sample script (examples/schlitter_determ.py) showing how to get the covariance matrix of your protein backbone, from which you can calculate PCA using numpy/scipy.

Naveen

----- Original Message -----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
Date: Monday, February 11, 2008 12:36 pm
Subject: Re: namd-l: PCA calculation
To: "Xu, Jiancong" <xuj1_at_ornl.gov>
Cc: ramya narasimhan <ramya_jln_at_yahoo.co.in>, namd-l_at_ks.uiuc.edu

> *Real* programmers use matdcd
> ( and do it in
> matlab. ;-)
> But gromacs is the fast and easy way way.
> Peter
>
> Xu, Jiancong wrote:
> > Don't think so. One thing you can do is to convert dcd trajectory to
> any other format that can be read by gromacs, and use gromacs to
> calculate PCA.
> >
> > Jiancong
> >
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu on behalf of ramya narasimhan
> > Sent: Mon 2/11/2008 2:49 AM
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: PCA calculation
> >
> > Hi all,
> > Is it possible to calculate PCA for MD trajectories using
> NAMD?
> > Thanks in advance.
> >
> > Ramya.L.
> >
> >
> > ---------------------------------
> > Chat on a cool, new interface. No download required. Click here.
> >
> >

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