AMBER Archive (2006)

Subject: Re: AMBER: PCA

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Sun Apr 09 2006 - 13:09:06 CDT

Am Donnerstag, 6. April 2006 22:27 schrieb venditti2_at_unisi.it:
> Dear all,
> there is a way to filter a trajectoy to diplay only the motion along a
> paticular eigenvector?

Have a look at the "projection" command in the "correlation and fluctuation
facility" part of ptraj: with this you can project snapshots onto modes
previously calculated and thus get the "amount of motion" of the molecule
along this collective variable. Is this what you want?

Best regards

Holger

> Thanks in advance,
> Vincenzo
>
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-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke

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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