[gmx-users] query on g_sorient
msanku65 at yahoo.com
Thu Jan 19 22:23:55 CET 2012
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 ?
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