Re: PCA calculation

From: NAVEEN P MICHAUD AGRAWAL (nmichaud_at_jhu.edu)
Date: Mon Feb 11 2008 - 12:37:07 CST

Just to get a sense of the MDAnalysis library, here are the example scripts:

http://code.google.com/p/mdanalysis/source/browse/trunk/examples/

And the schlitter entropy script in particular:

http://code.google.com/p/mdanalysis/source/browse/trunk/examples/schlitter_quasiharmonic.py

The example scripts are a bit outdated since they still use Numeric, but now MDAnalysis uses numpy internally and is fully compatible with the __array__ interface used by Numeric and numarray (but i recommend using numpy).

Naveen

----- Original Message -----
From: Peter Freddolino <petefred_at_ks.uiuc.edu>
Date: Monday, February 11, 2008 1:09 pm
Subject: Re: namd-l: PCA calculation
To: NAVEEN P MICHAUD AGRAWAL <nmichaud_at_jhu.edu>
Cc: "Xu, Jiancong" <xuj1_at_ornl.gov>, ramya narasimhan <ramya_jln_at_yahoo.co.in>, namd-l_at_ks.uiuc.edu

> Fantastic! I didn't realize someone had gotten around to writing a
> trajectory reader that works with numpy -- I'd much rather use
> numpy/scipy than matlab...
> Thanks for contributing this :)
> Peter
>
> NAVEEN P MICHAUD AGRAWAL wrote:
> > *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.
> >>>
> >>>
> >>>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:49:15 CST