[gmx-users] g_sorient -ro output
Laercio Pol Fachin
laercio_pf at yahoo.com.br
Wed Feb 25 03:38:19 CET 2009
I have a question about interpreting the output from a GROMACS tool, g_sorient.
I'm analising the solvent orientation around some specific atoms of my molecules, using GROMACS 3.3.3.
I have read the mailing lists, but I could not find anything specific about it (although the following discussions have helped me a lot, regarding which output - o, no, ro, co - could better answer my questions):
In addition, I could only find few references with such analysis, but I could not understand its meaning from them.
Concerning the -ro output, I have retrieved two different results, depending on the atom I'm analising: negative or positive values of cos(theta) distribution along hydrogen-bonding distances (2.5 to 3.5 angstrons).
As far as I could understand, g_sorient outputs:
(1) a negative value on the distribution around hydrogen bond distances, when water molecules are predominantly performing hydrogen bonds with the atom, as follows:
(2) a positive value on the distribution around hydrogen bond distances, when water molecules have their hydrogens pointing predominantly away from the atom, as follows:
Is my interpretation right?
Thanks in advance,
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