[gmx-users] g_sorient

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Wed Oct 22 21:54:01 CEST 2003


I am trying to use g_sorient to calculate the solvent orientation around
my solute. To test g_sorient I created a gro file the has one Atom and
one H2O molecule in  the following orientation.

A --- O

When I look at the output files for I see a distribution for theta 1
peaked at 90 degrees and a distribution for theta 2 peaked at 90
degrees. Three question: 1.) Why do I see a distribution? I would expect
only one point. 2.) Why is theta 1 peaked at 90 degrees? Based on the
definition in the manual it should be either 0 or Pi. 3.) Does g_sorient
normalize the angles.



Ilya Chorny Ph.D.         Department of Pharmaceutical Chemistry
Postdoctoral Researcher   University of California-San Francisco
phone: (408)-887-8496     Genentech Hall 600 16th St Box 2240
fax: (415)502-1411        San Francisco, Ca, 94107
            email: ichorny at maxwell.ucsf.edu

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