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
--
========================================
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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