Dear Professor Roe,
Thank you for your guidance.
>My guess is that the 306th eigenvector contributes very little
>to either system (i.e. the eigenvalue is very small compared to the first few
eigenvalues).
>My feeling is you should be focusing on the eigenvectors with larger eigen
values.
Yes, I agree with you in that first a few eigen values are important
to describe global motion of protein.
In the contrast, can we consider the eigen vector with smaller eigen value
represent fast mode, such like bond stretching between atoms?
They could be ignored if we focus on global dynamics of protein.
If so, it is clear that I should ignore such a fast mode.
Yours sincerely,
Ikuo KURISAKI
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Saturday, February 16, 2013 4:55 PM
To: AMBER Mailing List
Subject: Re: [AMBER] What algorithm does ptraj use for solvation of eigen-value
problem.
Hi,
On Fri, Feb 15, 2013 at 10:40 PM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> I found the pair of both 306th eigen vector showed the value close to 1,
> (e.g. 0.97). This indicates that the 306th eigen vectors are similar each
other.
I don't know how significant it is that your 306th eigenvectors for
two different systems are similar. My guess is that the 306th
eigenvector contributes very little to either system (i.e. the
eigenvalue is very small compared to the first few eigenvalues). My
feeling is you should be focusing on the eigenvectors with larger
eigenvalues.
-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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Received on Sat Feb 16 2013 - 00:30:02 PST
