[gmx-users] g_sorient -ro output

Laercio Pol Fachin laercio_pf at yahoo.com.br
Wed Feb 25 03:38:19 CET 2009

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):

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

(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:

ATOM       O


Is my interpretation right?

Thanks in advance,

Laércio Pol-Fachin

      Veja quais são os assuntos do momento no Yahoo! +Buscados

More information about the gromacs.org_gmx-users mailing list