[gmx-users] query on g_sorient

Sanku M 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 ?

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120119/0a350061/attachment.html>

More information about the gromacs.org_gmx-users mailing list