AMBER Archive (2006)

Subject: Re: AMBER: about atomic fluctuation & RMSF

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Thu Mar 23 2006 - 07:01:14 CST

Am Donnerstag, 23. März 2006 11:05 schrieb xueping:
> Dear all...
>
> What is the difference between

With
> analyze mode fluct
you can calculate rms fluctuations from normal modes (or principal
components). This requires to having done a normal mode analysis or principal
component analysis in a previous step.

With
> atomicfluct
you can calculate atomic fluctations directly from a trajectory. Note that you
need to rms fit the snapshots beforehand.

> Is atomicfluct same as RMS Fluctuation?
Yes, it is.

Best regards

Holger

>
> Thank you very much.
> Regards,
> xueping
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Juniorprofessur fuer Molekulare Bioinformatik

J.W. Goethe-Universitaet
Fachbereich Biowissenschaften
Institut für Zellbiologie und Neurowissenschaft
Max-von-Laue-Str. 9
60438 Frankfurt/Main
Germany

Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29527
Email: gohlke_at_bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
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