calculating angles between three points and distribution of them

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roja rahmani

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Jun 10, 2022, 12:31:05 PMJun 10
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Hi,

I have a nanoparticle and I would like to calculate the distribution of water orientations around nanoparticle. There are two types of angles:

1---  I want to claculate the angle consisting 3 points : first one is the center of mass of nanoparticle second one is the oxygen atom of water molecule and third is H atom of water.
So I need to claculate this angle for all water molecules in the box (or at least to the last spherical shell) and then get the distribution of angles.


2-- this time instead of considering H atom as one point I'd like to calculate the angle between dipole vector of molecule and another vector(one point is again center of mass of nanoparticle another one is oxygen atom). and again get the distribution of this angle as well.

I have looked up for angle module MDAnalysis.analysis.bat module but I don't know exactly it works for what I want or not. And how does it work when you have long trajectories? because I couldn't do some analysis and the kernel crashed probably because of long trajectory in jupyter notebook.

I would be appreciated if you have any solution.

Best,
Roja

Hugo Macdermott-Opeskin

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Jul 23, 2022, 1:49:02 AMJul 23
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Hi Roja, 

Hopefully this tutorial will help : https://www.mdanalysis.org/MDAnalysisTutorial/trajectories.html#exercises-4. In it a variety of angles are calculated. To get the distributions you can get the timeseries of the angles and plot a histogram.

Cheers

Hugo

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