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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)
*

*> >>
*

*> >> _______________________________________________
*

*> >> AMBER mailing list
*

*> >> AMBER.ambermd.org
*

*> >> http://lists.ambermd.org/mailman/listinfo/amber
*

*> >>
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*>
*

*>
*

*> --
*

*> -------------------------
*

*> 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

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:

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Received on Fri Jul 26 2013 - 05:30:09 PDT

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