Sorry, BTW, the slab is in xy plane. But i get an error when i use -g2 y or x .
How should i define the surface plane? On Sun, 9 Sep 2018, 14:45 rose rahmani, <[email protected]> wrote: > 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 [email protected].
