AMBER Archive (2007)

Subject: Re: AMBER: angle between vectors

From: Mag. rer. nat. Hannes Wallnöfer (hannes.wallnoefer_at_uibk.ac.at)
Date: Mon Dec 03 2007 - 01:55:51 CST

Dear Yildirim,

thats exactly what i want to do, but i don´t need the average angle, but
the distribution of the anlge values over the simulation. It would be
great if you could help to get this.

Best regards,
Hannes

Ilyas Yildirim schrieb:
> Dear Hannes,
>
> I once did a similar analysis for a system; analyzing the angle between 2
> different planes. I am not sure if amber has a script to calculate the
> angle, but I wrote a script to do that. What it does is, it calculates the
> vectors that are perpendicular to these planes, and takes the dot product
> of these 2 vectors to calculate the angle. For each .mdcrd frame, it
> calculates the angles and finds the average angle. Do you want to do a
> similar analysis?
>
> Best,
>
> On Fri, 30 Nov 2007, [UTF-8] "Mag. rer. nat. Hannes Wallnöfer" wrote:
>
>
>> Dear Amber users,
>>
>> i want to analyze the postion of two aromatic rings in my trajectory of
>> a proteine MD simulation. I was able to define vectors perpendicular to
>> the ring planes. Is there a possibility to calculate the angle between
>> these two vectors? I didn´t find anything like that in the manual.
>>
>> Thanks,
>> Hannes Wallnöfer
>> University of Innsbruck
>>
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>
>

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