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 Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
