AMBER Archive (2005)

Subject: Re: AMBER: RMS fluctuations along modes obtained from PCA

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Wed Jan 19 2005 - 08:51:10 CST

Majid moghaddam schrieb:
>
> Dear AMBER users
>
> I calcaulted RMS fluctuations along the first and the
> second modes obtained from PCA by the following
> commands:
>
> analyze modes fluct file evec.pev beg 1 end 1 out
> rms11
> analyze modes fluct file evec.pev beg 2 end 2 out
> rms22
>
> May somebody explain me the exact formule by which
> these fluctuations are calculated?

The computation is done in the section which starts with "Calc rms
atomic fluctuations" in the file analyze.c in $AMBERHOME/src/ptraj . The
constants used are defined at the beginning of this function.

> The fluctuations along the second mode are greater. I
> want to be sure that I have not made any mistakes. I
> would appreciate if someone helps me.

Does this hold for fluctuations of all atoms? In general, for increasing
frequencies, fluctuations should become smaller because they are
inversely related to the frequency (which is also the case in
analyze.c).

Best regards

Holger

>
> Best regards,
> M. Moghaddam
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

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
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