# Re: [AMBER] PCA Contributions

From: Pavan G <pavanamber.gmail.com>
Date: Fri, 26 Jul 2013 08:16:10 -0400

Thanks Dan. This is great help.

On Fri, Jul 26, 2013 at 1:00 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> Hi,
>
> On Thu, Jul 25, 2013 at 4:49 PM, Pavan G <pavanamber.gmail.com> wrote:
> > Should I then consider the inverse of each value?
>
> Not exactly. Eigenvalues are converted into frequencies with the
> following formula (you can see this in the code for ptraj/cpptraj):
>
> Freq = 108.587 * sqrt( 0.6 / Eigenvalue )
>
> The 0.6 is kT at 300 K in kcal/mol and the 108.587 is a conversion
> from Amber units to cm^-1. Hope this helps,
>
> -Dan
>
> > 5562 5562
> > 1 1/0.80680
> > 2 1/1.09819
> > 3 1/1.67464
> > 4 1/2.01560
> > 5 1/2.39907
> >
> > Then the contribution of eigenvector
> > 1 is 1/0.806 / [1/0.806 + 1/1.09 + ...+ 1/2.399]
> > 4 is 1/2.015 / [1/0.806 + 1/1.09 + ...+ 1/2.399]
> >
> > This would make sense. Is this accurate?
> >
> > P
> >
> >
> > On Thu, Jul 25, 2013 at 6:09 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> On Thu, Jul 25, 2013 at 2:20 PM, Pavan G <pavanamber.gmail.com> wrote:
> >> > But this would mean that contribution of 2nd eigenvector is more than
> 1st
> >> > eigenvector which seems incorrect since
> >> > 1>2>3>4>5.
> >>
> >> When you analyze mass-weighted covariance matrices (quasi-harmonic
> >> analysis) the eigenvalues are converted into units of cm^-1, so the
> >> smallest # in your case does correspond to the largest eigenvalue.
> >>
> >> -Dan
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 201
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-9119 (Fax)
> >>
> >> _______________________________________________
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> >>
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 26 2013 - 05:30:09 PDT
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