AMBER Archive (2005)

Subject: Re: AMBER: ptraj analysis

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Thu Jan 20 2005 - 01:28:27 CST


> I have some problem in ED analysis of my trajectory in ptraj.
> I used the following trajin script:
>
> trajin mdcrd
> rms first @CA
> matrix dist name distance @CA out dist-matrix
> matrix covar name covariance @CA out covar-matrix
> matrix correl name correlation @CA out correl-matrix
> analyze matrix covariance out evectors name evecs vecs 255
>
> The next problem are about "analyze modes fluct" and "anayze modes
> displ", Would you please tell me the physical or geometrical meaning of
> those commands and why the RMS of CA's for the bigger eigenvalues are
> smaller.

Try generating a massweighted covariance matrix (mwcovar) and
diagonalizing that one. In this case, eigenvalues are converted to
frequencies in cm^-1 before output, and low-frequency modes will result
in larger fluctuations than high-frequency modes with the analyze modes
command.

Best regards

Holger

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

J.W. Goethe-Universität Fachbereich Biologie und Informatik Institut für Mikrobiologie Marie-Curie-Str. 9 60439 Frankfurt/Main Germany

Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29826 Email: gohlke_at_bioinformatik.uni-frankfurt.de URL: http://www.uni-frankfurt.de/~hgohlke ++++++++++++++++++++++++++++++++++++++++++++++++++ ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu