[gmx-users] query on g_sorient

[Justin A. Lemkul]

Sanku M wrote:
> 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 ?
> 

Keep reading g_sorient -h, the reference group is explained.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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