AMBER Archive (2006)

Subject: Re: AMBER: PCA

From: Holger Gohlke (gohlke_at_bioinformatik.uni-frankfurt.de)
Date: Tue Apr 11 2006 - 07:27:26 CDT

Am Montag, 10. April 2006 16:57 schrieb venditti2_at_unisi.it:
> Hi Holger,
> many thanks for your replay.
> I would like to find a way to see how (not how much) the molecule move in
> the direction of a particular eigenvector.....something like the -filter
> option of the g_anaeig command in GROMACS.
> Do you know if there is something similar in AMBER?

No, this is currently not available.

Best regards

Holger

> Thanks in advance,
> Vincenzo
>
> > 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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> > The AMBER Mail Reflector
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>
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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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