Re: AMBER: ptraj analysis

From: Holger Gohlke <>
Date: Thu, 20 Jan 2005 08:28:27 +0100

> 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

Best regards


Dr. Holger Gohlke
J.W. Goethe-Universität
Fachbereich Biologie und Informatik
Institut für Mikrobiologie	
Marie-Curie-Str. 9              
60439 Frankfurt/Main            
Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
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Received on Thu Jan 20 2005 - 07:53:01 PST
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