AMBER Archive (2006)

Subject: Re: AMBER: PCA

From: venditti2_at_unisi.it
Date: Mon Apr 10 2006 - 09:57:41 CDT

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?
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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