Dear Professor Roe,
Thank you for your reply.
And I am so sorry for confusing question.
I took the following procedure to obtain the eigen values and vectors.
(1) MD simulations for both apo- and holo-protein were executed.
(2) Excluding environmental molecules (ions, waters and ligand),
I obtained two MD trajectories of the protein; each was derived from
different system, i.e. apo-protein or holo-protein system.
(3) The eigen vectors and values were calculated for both system
In terms of Ca atoms. Each trajectory was previously fitted on
The same reference structure. All modes were calculated; 306 mode for
306 degree of freedom.
Finally, I calculate inner products between each eigen vectors
for all possible, 306 x 306 pairs.
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.
So, my question is, is there any possibility that the last eagen vector
Has similar direction When we use ptraj to calculate eigen value.
Sincerely yours,
Ikuo KURISAKI
PS
> If you provide your exact ptraj input and output
> we may be able to provide more information.
I am really glad to hear your proposal.
But the trajectory files is so large, ca 13 GB.
Then I guess it is difficult way.
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Saturday, February 16, 2013 12:43 AM
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 2:08 AM, kurisaki <kurisaki.ncube.human.nagoya-u.ac.jp>
wrote:
> Would you tell me algorithm which ptraj uses for solvation of
> eigen-value problem,
If you're asking for all of the eigenvalues/eigenvectors in the system, ptraj
calls the dspev routine from LAPACK, which I believe uses the QR algorithm. If
you're asking for a subset of eigenvectors, ptraj calls the dsaupd/dseupd
routines from ARPACK, which use the Implictly Restarted Arnoldi/Lanczos Method.
> On the other hand, does the last eigen vector tend to take Some
> specific direction in ptraj?
The sign of an eigenvector is arbitrary, so I'm not clear on what you mean here.
If you provide your exact ptraj input and output we may be able to provide more
information.
-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 Fri Feb 15 2013 - 22:00:03 PST
