[gmx-users] g_sorient -ro output

[Laercio Pol Fachin]

Hi, all!

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):
http://www.gromacs.org/pipermail/gmx-users/2002-April/001374.html
http://www.gromacs.org/pipermail/gmx-users/2002-April/001375.html
http://www.gromacs.org/pipermail/gmx-users/2002-April/001376.html
http://www.gromacs.org/pipermail/gmx-users/2002-April/001377.html

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:

ATOM    H--O
            \
             H

(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:

             H
            /
ATOM       O
            \
             H

---

Is my interpretation right?

Thanks in advance,

Laércio Pol-Fachin


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