[gmx-users] query on g_sorient

[Sanku M]

Hi,

  I am trying to understand what are the angles g_sorient plans to compute. 
The manual says that the theta1 is "the angle with the vector from the first atom of the solvent molecule
to the midpoint between atoms 2 and 3" .  But, I wonder what is the reference position of this angle  ? In other words, what is the 3rd atom that one needs for the calculation angle ( the first atom being the water-oxygen, second atom being the  
midpoint of two water-hydrogen) ?  Is the 3rd atom any solute atom or their center of mass ?


Thanks
Sanku
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