---------- Forwarded message --------- From: rose rahmani <rose.rhm...@gmail.com> Date: Sun, 9 Sep 2018, 14:45 Subject: Gmx gangle To: <gmx-us...@gromacs.org>
Hi, I want to calculate angle between water molecules and ZnS surface(slab). I mean the angular distribution function(ADF) of ALPHA and BETA. I define to angles; Alpha= angle between OH bond of water and surface(plane) Beta= angle between HOH plane and surface(plane). I used gmax gangle for Alpha: Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh Then i selected water(SOL) group For Beta: Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh And again i selected water group. But results are little odd and histograms are two plot which are symmetric plots. I think sth is wrong. Should i make an index file for OH bond in the case of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it calculated the angle between COM of water vector and surface not the OH bond of water. As you know water has 2 OH bond. So... what should i do? How about BETA? does it really calculate what i want? Should i make an special index file? If i want to calculate this property (ADF) in for example 1 nm from surface, what should i do? To be more clear, I refer you to fig.1 and fig.8 roja: https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures Would you please help me how can i reach these goals? Best regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.